There are more ways to do 'good' endings than just rewarding players who refuse to give into the temptation. Yout had to *work* for your 'good' endings in Mask of the Betrayer IIRC. The 'pure' ending and 'god eater' ending both required you jump through some hoops to reach. Becoming a mindflayer with its consciousness intact like the prophecy foretold that people were speculating was going to be a part of the plot? could have been a special ending with certain requirements like using the tadpoles a lot, something you earned/worked towards instead of just a choice everyone got. Getting the tadpoles removed should have been one too, since that was something they said was going to be an option earlier in EA. Things in-between too.

You shouldn't make a game where the main driving motivation presented to the player is removing/using brain parasites and the consequences thereof and then just not engage with that plot hook except in the most cursory manner.