Teasing someone for being different doesn't qualify as a phobia. I'm sure all of the teasing and insults I got for being a redhead were just because I was unusual, not because people hated me.
And it's not that Renko necessarily hates homosexuality. It could simply be that her classmates were intending the accusation as an insult, and she was offended by their desire to ridicule. Even if she and Maribel were happily in a relationship together, she'd want to beat up people who were teasing them about it as though it was weird and wrong.
I'm pretty sure Chainsaw Guitar isn't talking about Renko's behaviour when he (or she) mentions homophobia, but her classmates'. (Also, it's not a clinical phobia, but it is the most common term for anti-homosexual prejudice and behaviour.)
Regarding which, yes, homophobia is everywhere - most particularly by the same sex (since they usually feel more threatened by it). I once read something describing the stereotypical young male as "can't get enough of lesbian porn, but they'd beat a faggot to death"; I'm sure the converse is frequently true of young women as well.
... and even in an alternate fictive future (for that is when Renko and Merry live, right?), the specter of intolerance still haunts everyone.
One cannot accuse giselebon of being subtle.
...the reason for her tears.Mary.We're just friends!Some heartless classmates of ours started spreading some baseless rumor that Mary and I were in a homosexual relationship with one another.I, in my anger at seeing my best friend insulted......got into years' worth of fights denying it.Mary and me?! You think that's the truth?!Shut up, lesbo.Don't insult my friend like that again!I was worried about the horribly shocked face I saw Mary make out of the corner of my eye, though.Mary, why are you crying?But it's okay now. The guys who were spreading the rumor promised not to do it anymore.I didn't understand......Thank you.It's a bit of an old story.Did I scare you? I'm sorry.Hey.C'mon, look at me?No... it's nothing.I'm sorry.