i am aware of counter-examples where hateful religious groups have moved into neighbourhoods and targeted sexual minorities in such a way that warrants self-defense against the religious community, but, broadly speaking, attacks on religious people are not a productive way to move society away from conservative religious ideas and towards a post-religious secular liberalism.
i tend to have a hard time denouncing people that destroy religious property, under a "diversity of tactics" argument. i'm probably not going to criticize you too loudly for burning a church down, if that church is promoting an anti-queer ideology, which they essentially all do.
but, violence against people does nothing to advance the causes of anarchism or atheism. it's counter-productive. and, while i know that most of the violence occurring right now is intra-religious, it is something for those that oppose religion to always keep in mind and be clear about.
as a species, we've tried rooting out religion by force repeatedly, and, whatever you think of the approach, the fact is that it doesn't work. you have to convince them...