Bending the tropes like that is out of Larian's ball park I assume. Or at least I very much hope so. But you can bet your precious behinds that we will get Dak'kon 2.0, with all the fanboying around Gith. I assume (s)he will be a DLC thing , but there is no way you have a story about Mindflayers without the Gith empire involved.
The zanyness of Baldur's Gate could even mean you get a benign illithid larva to insert into your choice of custom follower. Have the voice lines by the larva, but customize the follower being whatever you like and/or need.How about the opposite. An illithid turned into a human?