that doesn't negate the reality that religion exists, and that a community may need to defend itself against it should it attempt to enforce itself on it; it's not an argument for pacifism, or a suggestion that we should look the other way.
what it is is a tactical consideration.
and a request to be proportionate and reasonable.
you have to bomb isis, because they're indistinguishable from nazis, and they'll kill you if you don't kill them first. you can't reason with a hungry lion, you have to defend yourself.
but, that's the exception, and, most of the time, the better approach is to try to convince them that their god doesn't exist and that their rules are stupid and not worth following.