This is a universe with two canon male/male pairings. (Slash isn't the right term for them, since it's canon. "Gay" doesn't seem right either, at least not for Grant and Justin, because both of them had at least an adolescent interest in girls, even though they've since pretty much exclusively pair-bonded, and I'm very very reluctant to attempt to get into Justin's head as regards sexual orientation: even though he's fictional, it feels like he deserves at least that much respect for his privacy from me.) Yes, there's a lot of rampant heterosexuality; yes, Justin is surprised when Ari I has both Catlin and Florian participate in that "illicit intervention"; yes, Justin gets some static for pairing off with Grant. I read the surprise more for the group sex, and the static as trying any possible lever to Work someone, and a problem with his choice of partners (his Alpha companion rather than another CIT). From the other stuff, it sounded like heterosexuality is assumed until proven otherwise, but once otherwise was established, the fact of a same-sex relationship is not exceptionable.
I can see the role of homophobia in fictional universes. I can see the value in exploring and confronting it there. That form of homophobia, casual acceptance of a societal homophobic standard, does not seem to fit in that community, never mind what they think in Novgorod. Given that same-sex relationships are accepted at Resune at least once they happen, and that there's surely at least some biological component to it, I do not see Resune programming its azi to reject the concept. I also do not see either Florian or Catlin picking up casual homophobia from their environment.
It stood out to me. There are plenty of reasons why a sexual relationship with one's boss is a bad idea. There's never having given a thought to an intimate relationship with someone of the same sex before. (I surprised myself that way, though in retrospect I was indeed staring at my sister's violin teacher's tits an awful lot at age ~11.) There are many reasons why a CIT/azi relationship is a bad idea. Why having a relationship with someone for whom you're a bodyguard is a bad idea. So many different layers of possible wrong, and homophobia does not fit well enough into that universe that WHY PUT IT IN THERE, FOR FUCK'S SAKE.