I'm a huge fan of Annie Proulx, but I've never seen the movie. However, I read "Close Range," the collection fo short stories that includes "Brokeback Mountain," and I've heard her speak on the subject in interviews.
The story is clearly written from Ennis's point, and at the end, nobody is willing to tell him much of anything about Jack's death. He infers from their attitude toward him that he was beaten to death, and there's not much room to imagine otherwise. However, because it's all from Ennis's point of view, it's never stated outright by any witness.
Proulx seems to be rather annoyed by the "gay cowboy" characterization, first of all because (she says) anyone who knows Wyoming knows that there's a huge cultural gulf between sheep and cattle culture. These guys are sheep ranch handsd, not cowboys.
She's also annoyed by the singling out of that story. (She seems to get annoyed a lot -- she's a prickly New Englander who has addopted a prickly rural Western affect.) She intended the story as part of the collection, which she describes as a series of fantasies. There's something impossible and fantastic in all the stories, from the environmentalist rancher, the serial murderer in the desert 55 miles from the gas pump, the meth-addled youths, the mentally disabled sexual deviant, and so on. Everybody knows that none of that exists -- when of course it all does -- and everybody knows that there aren't any gay people in Wyoming.
It's not just a story about gay people; it's a story about people who aren't supposed to exist. Anyway, that's what the author said.