Taking a few pages out of the history books (or the newspaper, even), how about...
1. A kingdom has historically blocked gays from marrying, and the local church (who rivals the king for power, and has sole authority to perform marriages) has always supported this. However, a new, idealistic cleric has become high priest, and has started performing gay marriages. The whole kingdom is in an uproar - half the council is trying to pass laws against it, while the other half oppose such laws. The church itself is publicly divided - some priests embrace the new archpriest's policies, others accuse him of heresy. All sides contact the PCs, asking them to be their spokesperson or otherwise lend their support to their cause.
As an added twist, perhaps one of the king's own offspring is one of the first to take advantage of this.
2. In a homophobic city, there has always been a tavern which has the "worst-kept-secret" reputation being a safe place for gays and lesbians to meet and mingle. Every so often, the town guard will descend upon the tavern, arrrest the patrons for "public indecency" and make them spend a night or two in jail, roughing up a few patrons along the way. No one is really hurt, and it gives the guards something to earn their pay. One night, however, the gay patrons decide not to go quietly, but to resist. They have barricaded themselves inside the tavern, making a very public statement. The PCs are part of the mercenary group hired to put down the riot, or they have friends inside the tavern and want to help.
As another added twist, perhaps word of what has happened at the first tavern has spread, and the surrounding cities/taverns have also had problems with rioters.
3. A famous and talented playwright has been discovered to be a homosexual. It has become a highly public scandal. The playwright himself is unrepentant, as is his lover, a powerful nobleman. The conservative church is crying for blood, wanting the couple to be publicly punished. The more lenient ruling body, however, is shielding the playwright and his lover from punishment.
4. The PCs are hired by a town council to be the core part of a group being formed to eradicate a group of "evil witches" which live several miles outside of town in the woods (they're druids). The druids have been blamed for every wrong thing that has gone wrong in the town for years, most notably by one particular councilman, using the druids as a way to garner attention/support. No one told the PCs, however, that the druids aren't evil - they're merely lesbians whose lifestyle offends the councilman.
5. This one is really, really touchy and borders on being politically incorrect. For a mature group, though, it could be part of a really meaningful campaign. A slow-acting plague has gripped a kingdom - nearly every person who has caught it has died, generally not before passing it on. The plague barely responds to magical healing, and those who have died from it are extraordinarily difficult to resurrect. For some reason, the homosexual population of the city is hardest-hit, causing the fearful public to blame them for it. Events akin to medieval witch-hunts have occured - those known to have the plague, or known to be homosexual, are publicly executed and their bodies burned. Now, though, several high-ranking members of society have caught the plague - and a local wizard thinks he knows how to stop it.
6. A certain tribe of elves has traditionally respected gay/bisexual tribe members - granting them special status and believing them to be spiritually elevated, and capable of strong magic. The tribe lives in peace next to a city of mostly humans. The humans revile the elves' acceptance of gays, and have little to do with them other than occasional trade. Yet the son/daughter of an influential person has run away from the city to join the elves. The elves have accepted the person into their tribe and promised to protect him/her, but the parents are vehement about wanting their child back and "fixed" - to the point of, if they are rich enough, hiring mercenaries to go to war with the tribe.
7. The son of a rich merchant (or daughter) was caught "in flagrante delicto" in the arms of their same-sex lover. The outraged parents (who ascribe to a religion which forbids homosexuality in all forms) have hired the PCs to escort their child to a temple which promises to "cure" homosexuality - unbeknownst to the PCs, using methods of brainwashing and near-torture. Perhaps other 'patients' of the temple have contacted the PCs, asking to be freed from what is virtually a prison.
Hope this helps!