I like the addition of choice to side with the Mindflayers, but similar to siding with the Goblins in the main-game, I feel like a narrative reason needs to be added in.
By default, you currently side with the Giths because the "enemy of my enemy is my friend" (or at least a convenient tool to escape). Since you start off as an infected prisoner of the Mindflayers, there's got to be reason you'd want to choose them over the Gith.
Maybe an additional, non-hostile interaction with one of the Mindflayers in the beginning? He/she can at least give you a sales pitch (aka this Tadpole is a great honor, tons of power, etc).
To believe this, the character would have to lose half of his brain at this point. This makes even less sense when the character comes from the underdark.