It's fanon, but it's unfortunately plausible.

Homophobia is rampant in the American military. Homophobia is also rampant in the Black community, especially the church-going portion thereof. If you want to have that kind of tension in the story, Ford is a logical choice. It is actually (given his age, vocation, & race) more probable that he is homophobic than that he would be unfazed by finding out Sheppard was gay.