I think it's a little less of a leap to assume he is weak because they are being hunted and attacked by Gith, not because of some species wide cancer of anything.
He was not alone on the ship -- you pass by several Illithid corpses which appears to have been killed by imps, and there's a second Illithid at the helm who appears in the cut scene where he is killed by the imps as you enter the room.
The cinematic has the mind flayers dead before they reach Baldur’s Gate and before Avernus. It’s possible the gith killed them already but seeing the nautiloid was undamaged up to that point, I think that’s unlikely. The gith probably found their location because they abducted Lae’zel. Not that she’s meant to be important but that just says the mind flayers encountered the gith.
But yes, you could be right. It’s fun to toss out theories.
