Yeah, that may be the most dicey campaign outline I've ever created, but the truth be known is that I went there because I really don't think Mind Flayers make that great of villains. They make great monsters maybe, but they really aren't interesting to me as villains because they are just too alien. Their main scrutable motive is they think people are livestock, and so I went with that theme plus a villain that I thought would be more hateable, loathsome, and terrible because of at least his appearance of humanity.
You'd really have to handle that campaign delicately though, and you'd really need to know your players could handle it because the core issue is in a nutshell is: "Is genocide excusable as a means if the end is saving all of humanity?" That's going to be a potential mindscrew even without dealing with the sexuality issues. If you want more details on the campaign outline and where I'd go with it, let me know.