I was reading Why does religion get a special treatment in anti-discrimination laws?. Perhaps religion has a definitive clause somewhere in federal law, no doubt, and indeed religions are prevented from "overruling" each other in these so-called "free countries", but suppose there is a dispute between any two or more religions that begins to break out, perhaps even into incivility and even to the point of civil war between religions for matters other than political advantage (like the war of 1812 vs. the Catholic crusades against invading Mohammedans or taking back the Holy City).

My question is, apart from simply responding with military action when necessary, if there is law against discrimination of religion, and the above case were to happen in either Canada or the USA, or even both for that matter, how would the two governments deal with such a situation?

War is only an extreme example of what can come about from differing religious motives, but what about simply breaking the law by the discrimination of one religious group against another in civil matters?

The problem I see is that no one is allowed to discriminate religions, yet religions are at perpetual enmity with each other. How does the government reconcile irreconcilable conflicts like religious disputes in their own country? Would people committing acts of violence (or otherwise breaking the law) in the name of religion simply be tried for other crimes against the state to bypass their own anti-discrimination laws, effectively persecuting religions anyway, or would it be seen as mere civil disruption and hence considered persecuting individuals of the religion, rather than the religion itself?

(Note: any prohibitory law that might usually prevent someone from causing incivility or violence is not going to stop a religious group if they believe they are doing something for the good of their religion; I am looking for answers that specifically address potentially fanatical groups intent on breaking the law to achieve a religious resolution.)