Well i can think so many occasions when Freddie's homosexuality or flamboyance could have made the other members uncomfortable, taking notice that especially in the beginning they wanted to fit in the rock -world.
From the name QUUEN , to the adaptation of the mustache, to the on-stage over the top capmness, to the actual truth that he had a different sexuality from the other 3.Of course Roger, Brian and John are not your everyday individuals copying with homophobia like the stupid majority of youngsters, especially those days.
But still when egos and artistic differences came within, i wonder if that friction never touched that area of Freddie's sexuality even as a joke. Any incidents you know, would be very use full.
And from all accounts, both before and after Freddie's death, that he was gay never seemed to be an issue. Freddie's stage persona was mostly an act, fashioned out of '70s gender-bending (David Bowie, Lou Reed, etc.) with an aim to get noticed and make an impact. He was pretty shy and interverted in real life, so they say, with the exception of loving a good party (who doesn't?). Roger and Brian knew Freddie before they formed Queen, both as friends, fellow musicians, and with he and Roger working at a clothing store together. By the time Smile broke up and they formed Queen, I'm sure there were few surprises or "uncomfortable" moments like you describe. Maybe they didn't know he was gay at first, but he was their friend and as such, they probably just rolled with it. I've had friends come out of the closest and it's never been uncomfortable (for me anyway). They don't stop being the person they were and most times they're happier after they make that discovery or accept that fact (neither of which I can imagine is easy). As for John, who arrived after Queen came together, I'm sure the same was true.
Queen, as a band name, covers many things. It's a short, simple, memorable name. It's royal meaning is known in many countries and languages. Yes, it also has gay connotations (drag queen, flamboyant person, etc.) and I'm sure the band were aware of them, but it all ties into the image they were trying to carve, something memorable and in-your-face. A new band in the '70s, fighting for radio and TV attention will employ every trick in the book!
Most of the disagreements I've read about were music-related, in the studio, fighting over the direction a song should take, or about lyrics or individual parts of a song. I doubt it ever got so personal as you imply with your question. If it did, obviously they learned to get over it, or past it, because they worked together for over 20 years.
I remember reading that Freddie lived with Mary Austin for several years before he began to act strangely, and then finally told her he was gay, so I don't think it was even an issue in the first years of Queen, though I'd have to go back and check the dates to be sure.