Many of the people who came to North America in the first place came to avoid religious persecution.
This being the case; at the time the founding fathers added Freedom of Religion to the constitution; were there any religions in North America that would kill people in the name of their religion? And if so, how did the Founding Fathers weigh national security against Freedom of Religion?
TL;DR: NO but it's complicated
The question as stated is somewhat misleading, because "religions ... that killed in the name of religion?" is not an absolute yes/no category but is a continuum.
As examples on that continuum you have:
Aztecs.
This is where the religion itself centers on murder; with human sacrifice being demanded by the gods and a major part of religious observance
Islam
This is where religion itself doesn't demand murder per se, but largely blesses it in the name of converting the infidels and spreading itself. See Mohammed's conquests. What makes Islam special is that the conquests in the name of the religion are codified in the religion itself and the religious texts (e.g. the concept of Jihad).
Christianity
This is a distinct case, where the religion itself as it started did NOT condone murder in its name and was largely pacifistic. BUT, in the course of history, the religion morphed into a political organization that was Church, which fused with secular rulers. As such, religion was used to justify politically desirable murders, both in the service of secular powers (blessing the Crusades, which were really underneath a way to get rid of overpopulation pressure of junior knights - which is how Constantinople got sacked; or for than matter most witch trials which was a popular way to have people to get rid of those they disliked by witch accusations); as well as the political power of Church authorities (Inquisition, witch trials again).
Buddhism
With exception of one small branch, a very pacifistic religion, that was never used to justify killing (which is not to say its adherents never killed people in war).
Since there were no significant amount of Jews, Buddhists, Hindus, Shinto or Muslims in USA at the time, we are left with Christians and Native American religions.
Christianity
As @user45891 noted, by the time the Founding Fathers coined the First Amendment, the whole point was that the institution of Christian Church was reforming, largely as a consequence of both Protestant Reformation AND the pain of 30-year-war. So by the time the Amendment was done, the philosophical thought within Christian Church was specifically aimed at disassociating the power of the church from the power of the state - so the religion of Christianity as practiced in 1700s in USA was a lot closer in how it viewed killing in the name of religion to the "pacifist" spectrum end than to the way the Church molded it between 500 and 1500AD.
Native American religions:
First, plenty of them were centered around sacrifice, but most well known ones were (while in North America) outside what United States territory would be, or were more in Central America in the first place (Mixtec, Aztec, Maya).
Second, some Native American cultures practiced religious sacrifice:
Mississippian culture - the evidence isn't overwhelming but it's plausible. (ref, ref)
Eastern Woodlands tribes.
However it's important to note that the whole religion wasn't based on murder the way Aztecs' was; for any of these examples; and most wars were fought in the name of prosaic resource competitions or other politics and not in the name of religion, both inter-tribe and against Europeans.
The first amendment (That one related to Freedom of Religion) was added in 1791.
It's safe to say that the only notable religions in the US then were Christianity and various native nature religions.
There were several native North American 'religions' that justified killing for religious reasons - @DVK's answer has a short list.
But the Indians were seen as a political threat - the national security concerns were over all out war, not about them kidnapping law-abiding Americans for usage in religious slaughter.
(Also as the Indians weren't citizens this constitutional right didn't apply to them anyway)
But the Christians did it too.
The 30-year war ended only in 1648, during the French revolution (1789 - 1799) Catholicism was fought, the persecution of Jews, Catholics vs. Lutherans, ...
Even if not necessarily leading to be killed, not participating in the state church lead to severe disenfranchisement.
So yes there were - and that IS the reason religious freedom exists.
Each person for them self can choose what to believe in and nobody has any say into that - if not you're judging which religions are good or bad. And that always ends bad for some folks.
The Constitution was heavily influenced by Locke - who 'invented' the secular state to make sure no citizens could be infringed upon for their religious beliefs.
So no - they didn't weight it against national security because that was not related to why there exists Freedom of Religion in the US.
Yes, but it was probably considered uncommon by the time of the American Revolution.
Crimes against nature
Even after the American Revolution, statutes remained on the books of numerous U.S. states that imposed the death penalty not just for murder, but for some crimes of sexual sin, paralleling those in Leviticus 20, sometimes quoting directly from religious text. Details of enforcement are scanty, because they were considered "the crime not fit to be named among Christian men." However, lack of evidence is not evidence of absence. In some sense all capitol punishment might be considered killing justified by religion in any religion based on the Old Testament, we've just found alternate words to describe it. Others of course argue it is not justified, I take no position one way or the other.
Heresy
The Witchcraft Act 1735, was intended to end executions for most religious crimes under the laws of the Kingdom of Great Britain, but the practice continued to be permitted in other monarchies, typically for heresy, which we would view today as a religious crime. The primary example might be heresy against the Roman Catholic church under Spanish law.
The Spanish Inquisition had extended into New Spain (including North America) and was known as the Mexican Inquisition. That religious court was established in Mexico City and only abolished in 1820, as a result of Mexican independence.
By 1781 under Spanish law, heresy against the Roman Catholic church was still legally punishable by execution by burning, but that was generally considered unseemly, so heretics were sometimes granted the privilege of being strangled before the flames were lit.
Records of the Inquisition in Mexico are at best incomplete, however researchers have said that while the Mexican Inquisition only prosecuted a very small portion of the population, the persecution of crypto-Judaism was one of the more dramatic kinds of spectacles because they usually ended in death, especially during the early period.
In Europe, Cayetano Ripoll is thought to be the last heretic executed by the Spanish Inquisition, he was garrotted in 1826 Spain for teaching Deist principles in violation of the teachings of the church. So while it seems unclear if killings based entirely on religious beliefs were happening in the New World in the time of the founding fathers, they certainly had good reason to believe the threats remained.
Several of the US founding fathers were heavily involved with Deist principles including James Madison and Thomas Paine. The later is especially relevant as after the American Revolution, Paine moved to France, and during the revolution there was imprisoned and targeted for execution based on his own Deist writings collected as The Age of Reason. Paine was released only through the diplomatic intervention of James Monroe (another founding father and future president) in 1794.
Other founding fathers including Benjamin Franklin, George Washington and Thomas Jefferson were at least interested in Deist principals deemed heritical by the Catholic church. So yes, it can be said that questioning the teachings of organized religion of the day could result in a death sentance, and that fact led to inclusion of religious tolerance and freedom in the US constitution.
Anticatholicism in America
The story is not as one-sided as it might seem. It should be noted however that colonies like Maryland, founded by the Catholic Lord Baltimore passed the Maryland Toleration Act of 1649. However this was done in an effort to protect English Catholic settlers as the Catholic population quickly became a minority. The Puritans took power and permanently revoked the tolerance act until the American revolutions. During that time, the Catholics of Maryland were subject to persecution based on their religion with corporal punishment, though probably not death for heresy due to the 1735 act in Britain. But prior to that, a number of people had been executed in Puritan states, including a group of women known as the Boston martyrs who were condemned to death and executed by public hanging for repeatedly entering the Massachusetts Bay Colony as Catholics about a century earlier.
Treason and the Devine Rights of Kings
The European concept of the Devine Right of Kings held that a King received his authority to rule from God. In 1534, Parliament passed the Act of Supremacy and the Treasons Act, establishing correspondingly the King's religious position in the law, and making it an act of treason, punishable by death to disavow that supremacy. Though exercised in the 1500s, this law became dormant and religious tolerance in England took hold, but remained on the books.
In 1760 Francis Bernard became Governor of Massachusetts, and in 1765, he wrote that the King-in-Parliament retained power that was absolute, uncontrollable, and accountable to none, and therefore, in a political sense, can do no wrong. He also asserted that this applied unconditionally in the American Colonies of the Kingdom, regardless of their lack of representation in Parliament.
One of the final issues leading to the American Revolution was the Administration of Justice Act 1774, which George Washington and others referred to as the Murder Act, as they thought it permitted the murder of Americans through trials in England with no recourse. At the heart of such matters of sovereignty remained the core assumption of the Devine Rights, and that capitol punishment was still officially sanctioned by the Church of England.
Your question's lead contains a few misunderstandings which, when addressed, I believe answer the question. The misunderstandings I believe are in your question are that the Founding Fathers and the Christian Puritans held similar beliefs and motivations, and that the Puritans who "came to escape religious persecution" didn't, themselves, persecute other religious groups.
The early Puritans in New England (who are often said to have come to North America to "escape religious persecution") executed and imprisoned people in the name of their particular brand of Christianity in the previous century to the revolution. There were also the infamous witch trials. The founding fathers were by and large deists*, and were motivated by the violence they saw from theists (as opposed to deists) like the Puritans to separate church and state. Thomas Jefferson was quite hostile to established Christianity, even taking a razor blade to his Bible to cut out all supernatural claims, to leave what he considered the moral teachings. The founding fathers passed the Treaty of Tripoli in 1796 unanimously and without argument, which, crucially, explicitly states that "the United States of America is not, in any sense, founded on the Christian religion".
*Deism is basically atheism-lite: there is a god, but he just created the universe and then ceased interfering in reality at all: no miracles, no resurrection, nothing. This is the "creator" of Jefferson's Declaration of Independence.
In American history there are numerous accounts of religious people commiting murder in the name of God. Take for example the Salem Witch Trials and the Puritan's belief that natural forces were demonic.
Other incidents of such behavior:
...and many more but I am not allowed to post more than two links.
