Every time people lament changes to the lore that amount to "not every member of species X is irredeemably evil" and claim the game is removing villains from it, I think how villains of so-caleld evil species fall into two cathegories: a) bland and boring and b)have something else, unrelated to their species going on for them, that makes them interesting.
Personally, as a DM I get tired of how many different intelligent species there are. It makes worldbuilding very hard. I tried carving out space for each of them, but it wasn't worth it. These days I prefer to just get rid of most races, but it's a bit hard to tell which ones to keep.
Try flipping your process. Instead of working from the full list and taking things out, start from an empty list and add stuff in. If there isn't a good enough reason for it to be there, don't put it in. And if this leaves you with just humans, that's fine.
I'm not removing githyanki from my game. Githyanki were never in my game.