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.
