I've often pondered about how Vulcans view gender and sexuality.
I think pre-Surak/logic, they may have demonstrated homophobia and transphobia, but modern Vulcan Society would probably be chill with it under the reasoning that discrimination would reduce a person's efficacy as a functional member of Vulcan Society. For instance, given a choice between allowing a person to contribute verses driving them to the brink of suicide, Vulcans would probably tend to lean towards the first option.
There could very well still be stigma (Vulcans are far from a perfect society; some may have views that it is illogical to have a romantic relationship without a child), but it's dampened by the logic from the previous paragraph.
There's also the Pon Farr to keep in mind. Not only would it be hard to fight a person in the Ponn Farr, but also you'd literally be killing them by trying to prevent expression of their orientation.
Despite the storytelling potential, I’d think that the Pon Farr would put an automatic limit on any homophobia the Vulcans have, as once again, denying someone would have lethal consequences.
I don’t recall mentioning homophobia.
I also disagree that the inherent disregard of “illogical” alternative relationships or identities would be rooted in hate. “Hate is illogical.”
Though the idea that there is a Vulcan somewhere who is harboring hateful emotions towards Vulcans who identify that way would be yet another potential story to tell. Something akin to the Enterprise episode Fusion.