There's really no argument against the institutional and historical hypocisy. There's no shortage of people and groups that have done or currently do horrible violence against others, sometimes even in the name of these ideas.

But I don't know if that takes away from the idea itself and what fruitful counterpoint it might play in modern discourse.

So your argument is that if some people who claim allegiance to an idea do evil things, that renders all who claim such allegiance, and even the idea itself, evil? That is a pretty poor argument. It's also one that I don't think you would actually accept in another context. I bet you anything that I can find some ideal you uphold which was espoused by some vile people at some point, and I also bet that you wouldn't go "ok, I guess I have to give that ideal up now".