It's up to the player, if he/she wants to play an altruistic character that will help everyone, then the player will release Shadowheart Or the player could "RP" that the character doesn't know what the machine will do to Shadowheart, and thus leave her in. Alternatively leaving Shadowheart in the pod to die is something an evil character would do. But to respond to your first point: I don't think it's a problem that people free Shadowheart every time.
Your explanation for why the mindflayers leave Shadowheart in the pod with the gith weapon doesn't hold much water to me. It would be as simple as grabbing the artifact and placing it somewhere safe. And if an ilithid is indisposedm then have a thrall do it.
We both know the reasoning for why Larian did this: To few people doesn't use the tadpole powers. I personally liked the preavious iteration where they were a shortcut in order to obtain power, but felt like you did not get something substantial to tempt the player. That's why I am of the opinion that an ability score improvement and/or a feat for every milestone you reach in tadpole corruption is a better way to tempt the player. Not locking of Shadowheart away in the prologue to those of us that want to try a no tadpole run.
