I think now that extensions are out, and distros can start using them again, Ubuntu will make a comback.
Ubuntu doesn't even come with gnome-shell installed by default, why would they profit (much) from this?
I'm just speculating here, but it may well be the cause that John Haught said something under pressure that didn't accord with the teaching of the Catholic Church, and now he doesn't want it getting outthere.
If his job were to - as you speculate - rely on him remaining intellectually dishonest in public, I don't quite see how that's a redeeming factor..
Trying to be happy is like trying to build a machine for which the only specification is that it should run noiselessly.