I agree.
If he's really a homophobic, in college he's quite passive about it, as it's not like he grabbed a megaphone and complained to everyone on campus that the was "unfairly being forced to room with a homosexual"... While it is true that every little thing he said would definitely be used against him if he were to do something more actively hateful against Juna, on their own none of those would be serious enough to be called "a crime" (those may get him a warning, but criminal charges? Isn't that a bit of a stretch?).
Even about his "anti-fan" trolling, it's not like they would be able to prove that he systematically stalked Juna... It's not like he posted a thousand insults per day, nor that the majority of them addressed Juna's sexuality... nor that rallied an anti-fanclub to bomb him and his fans with incessant hateful messages. The worst case scenario would be he would be made to close the anti-fan account or stop posting about Juna altogether, with a slap on the wrist as a warning. I think in order for an accusation of stalking and discrimination to prosper, it would be necessary to establish that the victim was substantially harmed in some way (economic, social, etc) or that he had a credible reason to feel threatened somehow... but I think even law enforcement officials would laugh too much at the way the fangirls are torching the anti-fan and at the way he's only succeeded making a complete fool of himself, to actually bother with him... If his trolling was successful, or a more aggressive, it would be another story, but since it isn't... ┑(￣Д ￣)┍
Sorry, I don't know how being forced (OPERATIVE word, here, folks) to share a room with the person you hate (anti-fan, folks, NOT fan), only throwing slurs at ONE person for being liked by your FEMALE friend and crush, losing in every confrontation one has with the other, etc... is supposed to make the MC a stalker or a homophobia motivated douchebag. I'll give you troll and saying homophobic things but those can't really be dealt with by anti discrimination or bullying laws. In fact, the MC's situation is much like a person with extreme Tourette's syndrome. It WOULD be discriminatory and bullying to target someone like that with anti discrimination laws.
What I find even more funny is that people who dislike the MC have most likely read stories with more blatant stalking and homophobic descriptions yet ignore the issues they have with it because it's the seme doing it.
Finally, the word 'homo' is spread liberally throughout yaoi manga so it's funny you only have an issue with it when the person most likely adopting a position similar to the uke role in yaoi is doing it.
Thx.