RTD is in overall control of the series, and sets the agenda. But the main complaint about his "overuse" is when he sacrifices plot development in order to get his message over, rather than get on with the story. The whole is he/isn't he debate about Jake shows that at times you can get rid of a whole scene if need to, hence that particular reference is not integral. That's why in my opinion he lays himself open to acusations of bad writing, even when in "Midnight" the actual gender of Sky's ex partner is (probably) not relevant, and yes from any other writer it probably wouldn't have been comented on. Thank god he didn't write Wasp and Unicorn, the coment about how one character couldn't mourn the loss of another would have been ponced on like a shot.
On the other hand, just because he's gay RTD doesn't have to like lesbians, or women. A proper bigot could make the inference that as Sky thinks her ex is behind the attack, it's because she's a follower of Wika, and thus has unleashed a demon to wreak her vengence.
And for those who're interested there are at least three "gay" references in "Turn Left",
1) Bohemian Rhapsody, by Queen, which is integal to the plot, and also has some relevant lyrics to it. But a reference to Freddy Mercury has got to count.
2) Captain Jack, who will be in the rest of this three parter.
3) The bit about men falling for the blonde hair, streching it a bit I know.
Mind you on average you'd expect over 6% of any writers characters to be gay.
And one of the references in "Empty Child" was integral to the plot, and also the same kind of "things are so much better now" message as in TUatW. Still adultery though.