Well, the film would be homophobic insofar as it relays the book's portrayal, while Lynch could just have left that part on the cutting board, like he did with many other details. The Barron is indeed gay in the book, but is also a more nuanced character (even though the Harkonnen are pretty much a Big Bad Bunch). In the film his portrayal is just gross, you feel like he just earned power by brute force and malevolence, while in the book you know he is actually extremely intelligent, a fearsome strategist.
What I mean is, in the book his homosexuality comes with a more nuanced characterization, and isn't portrayed as one more repulsive behavior. But the film just shows us his most caricatural and repugnant sides. If Lynch showed him to be a total bookworm, it would feel equally disgusting, and given the character's other characteristics it would feel like the movie's saying "AND the guy's a fucking egghead to top it off !".
I'm not saying Lynch is homophobic, and indeed he's simply displaying what the book tells us. But since he's also cutting off everything that makes the Barron a bit more subtle than a Batman villain, the fact that he's gay ends up being the one cherry on a top of gross, while in the book it's just part of who the Harkonnen are : hedonists.