I agree with all of this. Even if the Harlan/Lily love is true and beautiful, it was not being handled well at all. If other students and faculty are registering complaints, something is wrong. And if nothing changes (if anything, I can see Harlan getting worse trying to hide everything), the school is sending out a horrible message.
I also hated how many times they had to remind us that Lily was no where near as smart as Harlan.