I still do not think the issue is that it is disturbing (in my opinion it isn't). It is just "gross" in a horror/gore-fest B-movie kind of way. In a way, it is even comical and silly, that our character would just... grab into a skull to wiggle out a brain like that. It does nothing to make the Mindflayer thing creepy, it actually distracts from all that with cheap gore/in-your-face grossness. In light with what else is shown in the game and how other events that are meant to be creepy/disturbing are handled, this scene just looks out of place. Not in a good way and not creepy at all, it makes it hard to take the scene or this intellect devourer seriously, which is kind of the opposite of what is intended (the intention being creepy stuff, I figure).
For me, it kind of breaks immersion and it makes it harder to take the main character seriously too, for just grabbing into a brain after waking up in a alien ship that is literally in hell, where you want to likely escape from. I skip that part for this very reason, not because it creeps me out.