To me it seems like calling that the fault of "religion" seems roughly analogous to blaming the concept of "government" for the actions of a specific city or state/province government? (that is, either 1 or 2 levels below a national government , though I might have made a mistake with the analogy there)

Not all religions/versions of a religion are the same.

I acknowledge that an analogy is not always a particularly strong argument, but it was the first responce I thought of, and it seemed an acceptable responce to me.

Also, it might have made more sense to respond a few levels up, not sure what would have made the most sense to reply to.

It isn't a bad analogy. My counterargument is that local government policy can usually be changed a lot more easily than religious dogma, especially dogma surrounding who to demonize. Maintaining a strong notion of who is in the in-group and who is in the out-group seems to be an important mechanism in maintaining tribal cohesion.

My point is that religions seem prone to demonizing people as a quick and easy way to define themselves and maintain cohesion. Look at all the really nasty doctrinal splits through history.