I recognize that the concept is bad, because it says that physical deformities are a curse--the original caliban were mostly of the hunchback/clubfoot Igor type. It's a good thing that they're not in the book, because of this. I have zero problem with them being removed.
Nevertheless, I like the basic concept. The idea of being marked at birth with a curse is a good one for a gothic horror setting. It's just that specifying that certain actual, already marginalized people are actually magically cursed isn't cool. So I made a homebrew version, which I'm actually in the process of revamping, that removes that. For this, I combined many different things: other ideas that were in the books (such as the wailing ones from Mordent, or Shih Suren, a caliban that looks like an anthro-tiger, from Heroes of Light), and some stuff that was in an issue of the Quote the Raven RL fanzine. To that, I mixed in "real life paranormal" stories about things like black-eyed children or some of the weirder men in black sightings and the idea of people who look full uncanny valley (both a few real people who've used a lot of plastic surgery to look like dolls, and anime characters). While you can still play a caliban with physical deformities, that's 100% up to the player. It's not a requirement, like it was in the book.
So there's no cognitive dissonance here. I took an idea I liked, removed the stuff I thought was bad, and added stuff I liked, and above all, I know what my players are like and what is or isn't acceptable with them. And I'm still glad that WotC removed the caliban, because I feel that they had too much baggage to be brought over officially for the masses and aren't actually necessary for the setting.