Harris's quote - and objections to it - really do depend on making judgements about which is worse... though I do agree with you about it being rhetoric to create an emotional reaction.
I do agree that it would be needlessly nit-picky to somehow quantify all of religion's harm and compare it to the quantified harm of all the rape in the world (or at least all the rape that would persist without religion). I think the point of what he said is to call attention to the fact that the harm inflicted by religion is staggering.
There's no real-world scenario where people would stop trying to combat rape in order to focus on religion; the real issue we're dealing with is that religion is singled out for praise, special benefit, and tax breaks, and isn't generally pointed to as a problem at all.
The core point I think Harris was trying to make--that is, pointing out how destructive religion has been at different times in human history--could have been made using a better, more thoughtful, and more meaningful argument. It seems to me that rape is already normalized and excused enough in different societies without comparisons that employ it as a tool to gain emotional momentum.
Harris has intelligently and articulately laid out criticism of religion on more than one occasion without resorting to such emotional rhetoric. I view the quote in question as one of his worst blunders.