I was reading https://politics.stackexchange.com/questions/33396/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" eachother 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 politcal advantage (like the war of 1812 vs. the Catholic crusades against invading Mohammedans or taking back the Holy City). 

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?

The problem I see is that no one is allowed to discriminate religions, yet religions are at perpetual war with eachother. How does the government reconcile irreconcilable conflicts like religious disputes in their own country? Would they simply be tried for other crimes against the state to bypass their own anti-discrimination laws, _effectively persecuting religions anyways_, or would it be seen as mere civil disruption and hence considered persecuting individuals of the religion, rather than the religion itself?