Yea, there absolutely must be a 'good' reason why were encouraging the tadpole. I'm just not convinced that the reason will feel logical in any sense. I'm dreading that it will be another Withers moment, where everyone just sort of accepts them for reasons, but gameplay wise it's useful.
I have my doubts with Larian's writing, but they will acknowledge it somehow.
The reasons really are self explanatory: 1) we have this guardian figure telling us to draw more and more on the tadpole while promising to protect us from it and 2) there is a lot of power to be gained from it. The reasons aren't difficult to see.
Another reason that the game never explicitly states could simply be that ceremorphosis would be extremely unlikely to complete with multiple tadpoles in your brain...you'd definitely still die if the stasis holding them back was removed but you probably wouldn't turn into a mind flayer. So that adds a bit more sense there...you gain more powers and if you don't find a cure at least you probably wouldn't turn into a mind flayer.