Have a same-sex relationship. Simple as that. Don't have it be something that's asserted or made speeches about, just present it as part of the character's life, in the same matter-of-fact way you'd present a heterosexual character's attractions or romantic involvements.
In other words, do exactly what Trek Lit has been doing with gay/lesbian/bi characters for years already.
I agree with Christoper entirely. That is what I would expect the mainstream viewpoint of homosexuality in the fictional 24th century of Star trek would be.
By then they would know that a certain percentage of the human population would be born with homosexual tendencies, they would have no cultural stigma attached towards the expression of those tendencies, and they would be fully integrated into society.
So if character A or B was a homosexual, any inclusion of their personal life would be rather blahh 'Character A went to his quarters and talked about the tachyon monsters devastation of the Hakkonian planet with Character B before kissing him goodnight and taking a sonic shower'
Most of the normal "romantic" interactions in the novels would also be rather easy to adjust by simply changing the gender of personal pronouns.
Now the hard part would be managing the expectations of the 21ST century audience. Some people would be uncomfortable with overt sexual activity between homosexual characters (although the Star Trek novels are pretty mild in the whole "sex scene" department). And others are very eager to see more homosexual characters as part of their general view that modern fiction should reflect a modern "tolerance" for homosexuality.
My personal view is that the authors should use whatever character relationships that best fit the purpose of writing an engaging and entertaining story.
When external pressure causes them to sacrifice a good story to fulfill some expectation, then all the fans suffer.