I liked China Mieville's Judah character in the Iron Train, but he made it clear quite quickly that the character is gay and it affected the storyline in the same way any heterosexual relationships would have done. Presented with nonchalance and then used in the plot as something utterly normal, your bad guy's gayness could fit right into the story.
On the other hand, if the readers don't know he's gay from the start, they will probably already have placed the "bad guy" in one of the "bad guy" stereotypes. This will make them have certain expectations of the character throughout the story. And i don't think too many people would have "gay" as part of the stereotypes associated with the "bad guy". See where i'm going with this ... ?
Like everyone was a little ... uncomfortable with Dumbledore being gay. It's ok .... but i think a lot of people were asking themselves "couldn't you have left this one bit of information out , Mrs Rowling ?" It's ok to be gay, it's stupid to dump after the last book is out.After writing 7 damned books in which you failed to mention this in the slightest.You just made a legion of fans go back and say "aaah, so that's why Dumbledore did this or that" lying to themselves that anything in the 7 books even hinted to gayness. But suddenly the internet is full of people claiming they said he was gay after the second book, other after the first, some claiming to have known he was gay after reading the first chapter and have their personal journals as proof. But the more likely story is one of image, 17-18 yo average Susan and John's image of the gay community as a whole to be more precise. The kids who grew up reading Harry Potter are now in their late teens, and even if this doesn't look like much, as a social psychologist i can tell you this small announcement alone has made gay totally ok in the minds of many, many forming adults. Not make them want to be gay or even curious about life up the other end, it only made them truly understand that gay people are just that PEOPLE. It's a lesson no school will ever be able to teach to a kid that hears even moderate homophobic jokes in the family.But Dumbledore being gay ... it's like your grand uncle Freddy was gay, the nice uncle that always brought you the best stuff and never bothered you.
And even if this was a calculated move, for the people that loved the novels, as novels, not life-guides, it was a forced smile of acceptance. You can't say you actually didn't like him being gay (not because you have a problem with gay school headmasters who might or might not have abused you when you were in secondary school) just because it didn't fit in with the Dumbledore in YOUR mind, not in Mrs Rowling's

But i guess that's like the biggest taboo in western culture next to saying women should travel strictly by bus so as to free up traffic, and can only vote in two elections : the one for class president when they are in school and and the one for neighborhood president as adults and they can't run for either so they wouldn't vote with their tiny, less evolved brains (a clear example of this being the shameful 2004 US Presidential Elections, when women voted 51% for John Kerry, but the 55% of every castrated, emasculated, MAN voted for genius to run the world, good ol' doub'ya,while four years back, the elections would have been a no-brainer on the winner, women having no less then 29% more votes for the candidate who could actually spell the word spell;in fact, digging a bit deeper into gender difference data on elections, which is scares to say the least, one can clearly see the last couple of decades free of war, teaaaa'r, economical crises of such magnitude or just simple retard-ness if the Americans would have just listened to their women; if one needs more convincing into this women + politics = everyone'sahappiercamper business just write angela merkel on google and read the wiki; note that Germany dealt with this economical crisis stuff quickly and painlessly, aiding the companies to make more jobs, so they can hire the people they let go from the administration, problem solved in less then a year;i'm sure even the obama choice was the wrong one taken, again by the men, i'm very sure hillary would have had a tone more balls in washigton and things would have looked a lot better for the entire world) or something like that, you know what i mean, right?
So basically my advice to you is to read The Iron Train again, carefully noting how Mieville uses the main character's gayness as just another part in the story's structure, and yet, it fits so naturally and perfect in the storyline you wouldn't have it any other way.
Note that "Miéville is a modern Marxist; for him gay people are commonly just another part of a popular front of misfits against the powers that be. He treats Judah and Cutter and every other gay character in the book matter-of-factly, if without true understanding of was being gay is like"
If you think you can really integrate the gayness into the story, do it man. It's a sure bet to get some extra books sold on amazon and a bit more coverage. I think many people suffer from some form of suppressed guilt for gay people and in response will do stuff which has anything to do with gay.Like 70yo's going to gay parades to show support or going to see Brokeback Mountain at the cinema so they can tell every water-cooler friend that they were impressed and touched, even if it bored the crap out of them.If it's a bit of latent homophobic guilt that gets you in the hands of a big critic and shoots you to stardom, then don't hesitate to ride that train
Done a bit of reading for ya, so i hope this helps,
Cheers from Romania
p.s. i blame the damned weed for any incoherences or plain dumb things and credit myself for anything attention-worthy in the stuff above. please note that i have gone from discussing epic psychosocial chances what will probably affect the western world in unknown, but likely positive ways, done with a simple announcement, to the small bit of trivia that should women would have been the only ones with the right to vote , to pointing out queerguilt - which is better just cuz is sounds more British .
das ende