Disclaimer in PHB or dump inspiration list.
Or simply amend the list to actually be stuff to read to be inspired to play D&D. Like I said, it's not a bibliography and D&D is hardly an academic work. There's no need for the list to be complete (and it obviously isn't as is). Put stuff in that is actually inspirational instead of just shotgunning every big name in the genre regardless of history.
One of the biggest ironies in this thread is seeing how people said that 4e drove them away from the game. That the rhetoric surrounding 4e made them feel unwelcome. Almost as if the rhetoric and words we use in and around the game matter...
But, all that aside, having taken a very deep breath and lurked for a couple of days, I do think that the question of "what to do" is a fair one. Now, that being said, what I, personally, dude with no actual power can do? Not much more than I am - agitate and promote particular viewpoints and contribute (hopefully constructively) to the conversation. There realistically isn't a whole lot more I could do.
If I was WotC though, this would be what I would do:
1. Keep the disclaimers. They raise awareness. They aren't the be all and end all, but, they do serve a function. There's no reason not to do it, frankly.
2. I would hire a genre historian, like, say,
Amy H. Sturgis to write a regular column in Dragon+ talking about the history of the genre and about how that intersects with D&D. This would be an ongoing column.
3. I would not go back into the library and start editing material. The historical argument is a very strong one and I don't think it serves a purpose to try to rewrite history.
4. Related to 3 - However, since profiting off of this material is pretty icky, I would take the entire library of Pre-WotC, TSR, and put it online for free in some sort of format like Anyflip (where you can't just download it, at least pay lip service to protecting the material) for historical purposes. That way the material is there, it can be referenced, but, no one is profiting from it. And, it links back to 2 where it becomes very easy to clearly demonstrate where the problematic material is.
Anyway, I was asked what I would do, and, yeah, if I had the power, this is my solution.