I think he was indeed excluded for the suspected reasons. He was definitely one of the elements of the film that has been criticized by some as "problematic". And he has been making fewer and fewer appearances in the parks from what I hear. It wouldn't surprise me if he's phased out eventually. He's not quite as much of a concern as Splash itself, but the fact that the best and most universally popular thing about the film is absent from the ride is very telling.
How Mama Odie managed to escape this same criticism is beyond me. I really love her and she's an endearing and entertaining character (I even know people IRL like her), but she's the embodiment of a racial stereotype. Also surprised Big Daddy and Charlotte haven't gotten a similar thrashing from people and an exclusion from the ride. Again very fun characters, but they're wealthy sugar barons. I probably don't need to elaborate on the morals and dark history of that profession especially from that time period.
Another factor in Facilier's exclusion is likely related to Disney's softening of "scary" elements of kid friendly attractions. Particularly the reduced presence of villains in new and redone rides. Gaston being relegated to a shadow projection in the background of Tokyo's BATB ride is one example. Or the further softening of Snow White's Enchanted Wish. Not including Facilier seems to also reinforce that trend.
Including Facilier in TBA would have fixed some of the more glaring issues with the ride. Make the third drop function as a portal into the "Other Side", and have Facilier appear in spirit form in his skeleton makeup. This would have been an incredible opportunity to use a lot of contrasty black lighting. Could have been a very visually striking room. Ray could even be included as a friendly spirit trying to guide us back up the lift to safety, ample opportunity to include some really nice looking fiber optics for the firefly effects. Mama Odie still serving as a means to pull us back into the living world via the big drop. The final lift and big drop itself would also retain the dark tension it had in Splash.