We know there was supposed to be negative ramifications for using them. IIRC there even was datamined voiced lines about Nere and him taking control of you if you refused him while having heavy tadpole usage.
There's also still at least one line left over from EA for using the tadpole powers to convince enemies-the one about 'losing part of yourself you'll never get back' If stuff like that wasn't heavy foreshadowing, I don't know what is.
We know Rafael was going to be one option (perhaps a last resort option) to remove the tadpole, but there was going to be others, as well as the notion of just keeping the tadpoles and seeing how far that wild ride would take you.
