I believe the framers of the US constitution wanted to copy the good parts of British and colonial government and abolish the bad parts of British and colonial government.
And - at least according to the Declaration of Independence - they believed one of the worst aspects of British laws was the ability of the government to unfairly convict people and enforce arbitrary and unjust punishments on the people unfairly convicted.
And in those days British justice could sometimes be very arbitrary and more like "justice".
For example, the British government used a very broad definition of treason, and if the British government wanted to try someone for treason would stretch even that broad definition as much as possible to arbitrarily claim that person's actions were treason. And it might try those persons in a kangaroo court biased against them to ensure they were convicted.
And the British government could get the British Parliament to pass bills of attainder against persons, which were laws decreeing that someone was guilty of treason without any trial taking place. And at that time the property of convicted traitors (who were often very rich noblemen) was confiscated by the British government instead of inherited by the traitor's heirs. And at that time the maximum possible British legal penalty for treason was still a very horrifying and painful death.
And so Article III, Section Three of the US constitution says:
Treason against the United States, shall consist only in levying war against them, or in adhering to their enemies, giving them aid and comfort. No person shall be convicted of treason unless on the testimony of two witnesses to the same overt act, or on confession in open court.
The Congress shall have power to declare the punishment of treason, but no attainder of treason shall work corruption of blood, or forfeiture except during the life of the person attainted.
And for similar reasons the Fifth Amendment to the US Constitution says:
No person shall be held to answer for a capital or otherwise infamous crime unless on a presentment or indictment of a grand jury, except in cases arising in the land or naval forces, or in the militia, when in actual service in time of war or public danger; nor shall any person be subject for the same offense to be twice put in jeopardy of life or limb; nor shall be compelled in any criminal case to be a witness against himself, nor be deprived of life, liberty, or property without due process of law; nor shall private property be taken for public use without just compensation.
And the Sixth Amendment says:
In all criminal prosecutions, the accused shall enjoy the right to a speedy and public trial by an impartial jury of the state and district wherein the crime shall have been committed, which district shall have been previously ascertained by law, and to be informed of the nature and cause of the accusation; to be confronted with the witnesses against him; to have compulsory process for obtaining witnesses in his favor; and to have the assistance of counsel for his defense.
And the Seventh Amendment says:
n suits at common law, where the value in controversy shall exceed twenty dollars, the right of trial by jury shall be preserved, and no fact tried by a jury shall be otherwise reexamined in any court of the United States than according to the rules of the common law.
And the Eighth Amendment says:
Excessive bail shall not be required, nor excessive fines imposed, nor cruel and unusual punishments inflicted.
So the Americans in that era knew that they needed laws and courts and punishments, but also believed that they had to restrain the government from inflicting arbitary, unjust, and cruel punishments. So designed a system that they hoped would eliminate the ability of the executive department to achieve unjust convictions. The power of the chief executive to pardon did not seem like a dangerous power that needed to be abolished to them, even though it might sometimes be used arbitrarily.
That it is better 100 guilty Persons should escape than that one innocent Person should suffer, is a Maxim that has been long and generally approved.