Not a negative spark necessarily, but judging by the standards of D&D's the pseudo-medieval backdrop, it makes the most sense to me, personally. Then again, I run my games a little like a Jack Vance novel, in which 100% of the NPCs are corrupt, scheming, or tyrannical.
As for presenting homosexuality is a positive light, I'm all for it, as long as it furthers the story in some way. The PCs having the choice to stop two gay blacksmiths from being burnt on the stake and dealing with the repercussions of their actions or inaction could be interesting. Preventing a grove of druidic terrorists, who see homosexuality as an act against laws of nature, from hunting down and murdering homosexuals could be, too.