You are correct, the Mormons were armed; but more dangerous to rabbits, squirrels and deer than to the general population. Despite having an extermination order placed upon them, being forced at gun-point to leave their homes; the Mormons were then called upon to fight in the Civil war against the Confederacy (which they did).
The Mormons fled to Utah, where they were able to celebrate the 1st Admendment, but historically speaking, not without other outside 'Christian' harassment.
My point is that Christians cannot say "But we have never bothered them", as that statement is false, and patently untrue. Christians have a rich history of forcing others to their will. Now, the shoe is being placed upon the other foot (and again, historically speaking) once again.
Is the athiest correct in his approach? IMHO, no.