Oh, it looks like I forgot to actually address the OP… let me fix that.
Even with Shooter forbidding gay characters, it didn't stop writers like Byrne and Claremont from sneaking it in with plausible deniability; so I think if their hands weren't tied, they would be less vague about it. They might not be explicit about their gay characters— the Comics Code Authority, which still held sway at this point, also forbade non-heterosexual relationships— but they could push the subtext further and write characters as all-but-out (just avoiding certain words). Prime candidates here would be Northstar (whom Byrne said he always intended to be gay), Mystique and Destiny (whom Claremont intended as lovers and Nightcrawler's biological parents), or Kitty Pryde (whom Claremont always writes as bisexual).
But here's an idea: there was a Northstar story in the early 80s where he was dying of a mysterious illness, and legend has it that writer Bill Mantlo intended for it to be AIDS— but Marvel got cold feet and forced a last minute change into something else. Let's say Marvel goes through with the AIDS storyline, but the CCA objects, and Marvel does what they did a decade ago with the "Spidey vs Drugs" story: shrug, remove the CCA logo from that issue and publish it anyway. The issue causes a stir but is overall successful and acclaimed for its depiction of a sensitive real-world concern… and the CCA trying to kibosh it becomes a huge embarrassment for them and hastens their demise.
