I think the best case for New Atheism is that, under the current norms of American politics, holding a morally reprehensible event inside a house of worship means that any protest against it will automatically backfire.
This is compounded by the fact that, if protesting outside a synagogue is widely seen as antisemitic, the people who show up to such a protest will be disproportionately antisemitic!
I think Hitchens et al (whatever other issues you have with them) understand this extremely well, and their project is best read as an attempt to end the deference given to "religion" in Anglophone political life.
