I think a lot of folks are taking this way too seriously.
Guy being forced to dress up in girl's clothes and then fending off the advances of a guy who thinks it's a hot chick is an old, old literary/cinematic trope. "Body and Soul" was just basically a twist on that. I loved it because of the great performance from Jeri Ryan, who finally got to play someone with a personality.
I'm getting a little tired of turning every aspect of an enjoyable, sometimes thought-provoking show into a disputation on race, class, and gender.
Homophobes are the assholes who victimize people who are minding their own business just because of their sexual orientation. Anyone who calls someone who wrote, directed, or acted in a mistaken-identity romp homophobic is doing a real disservice to those who've really suffered homophobia. If you keep using the word to describe something innocuous but whose taste you personally question, it will lose any value it has.