There has been some conjecture (some by me) that the reason we don't see gays in Star Trek is because they are in some way being "suppressed" by the Federation's overall society. Think America sixty years ago. So having a Captain who make the decision to be openly gay would be one way of introducing gays into the Star Trek world.
The story line could mirror the historical gay coming out that actually occurred in our society, but set in the Star Trek universe, a on going B-story, or C-story that is one aspect of the series, but not the only subject of the series.
The Captain could meet with acceptance from some, but rejection, resistance and condemnation from other in Starfleet and the Federation on general. And even those aboard his (her) own ship.
This would be an alternative to suddenly showing gays and saying oh yeah "they" were alway here, and alway accepted.
The Federation is all inclusive, please don't ask too many questions.
I really don't see this as a viable way for them to bring homosexual relationships onto the screen... Starfleet obviously doesn't have a problem with mixed race / species relationships... as evidenced by the amount of half whatever characters around... and it's perfectly logical to assume that there are aliens in the Trek universe who have more than one sex... male, female, whatever else... i'm sure at one point it was said the Andorian's had 4 sexes... so limiting relationships to male / female wouldn't really work for an organisation like Starfleet...
I'd rather just have it included and passed as just part of the character... doesn't need to be any big fuss about it or anything, in 300 years or so, i damn well hope we're over homophobia and ignorance... if not then i really hope the first alien culture we come into contact with, blows the hell out of this planet for it's continued stupidity