I think they want to kill you because they don't want tadpoled people just running around. Something about your escape interrupted the previous process -- none of the other tadpole bearers are aware they are carrying them, but you are, and that makes you a threat to the conspiracy.
And by killing you they can collect the tadpoles and try again. With the loss of the nautiloid they might have lost their "science and development" base, so to speak. They might not have another way to develop the new kind of tadpoles.
Wait wait wait, let's rewind to do the circular narrative thingy again, see how this plays.
The first tadpole that you encounter after being infected is Us, the cute brain. Right away, you get the option to "cripple it", should it become a threat, or to leave it intact. I always leave it intact, poor pet. However, regardless of what you do, Us is already plugged into the Illithid Daddy's brain, fighting for his life at the helm, and knows exactly what to do.
This could be a foreshadowing of how the Absolute cripples the other brains, so that they become subservient to Her. Maybe that's what happens at Moonrise Towers, a kind of mystical brain injury. In Gut's case it went really badly. Alternatively, this could reference how you might injure your own brain accidentally, reducing your own agency and power. Volo's failed operation looks a lot like a lobotomy, after all. And this game LOVES to play with parallels, presenting the exact same action performed by different parties to deconstruct concepts like "good" and "evil".
Then, you encounter the other tadpole that is trying to escape from True Soul Edowyn -- the little beast reaches up, a bit like the worm in Labyrinth, a tiny high five to a friend. The scene is incredibly effective, because the camera shows your face from the tadpole's perspective, curled up in disgust, as the narrator explains how pure and adorable it is. The smart move would have been to remain in the cadaver until you moved away, but the tadpole itself doesn't perceive you as a threat, although to be fair it was pretty young.
