Personally I find it refreshing since ingame there is just no way of knowing whether or not there will be consequences same as in real life - it's a gamble.
Also I would argue that using tadpole powers while somewhat repulsive is not evil per se but pragmatic decision to use every power available against a formidable army of enemies - it also stands to argue that not using them could be counted as somewhat irresponsible or ignorant at least later in the game when there is tangible evidence you'd have been a mindflayer a long time ago without the prism/Emperor/Orpheus so like it or not - you do owe him.
And there is a matter of Astral tadpole that a PC who has never dabbed into tadpole powers can simply refuse while the others need to pass some pretty steep dicerolls and possibly turn into something against their wish - I'm pretty sure that's something one would percieve as pretty big punishment RP wise.
Better endings? Why? It's highly debatable and even less provabale you get a better ending by being a good person IRL - so why should THIS game be any different, it's a moral and philosophical decision which I find highly refreshing, just because we're used to cliches in games/movies/books certainly doesn't mean they should be followed or that a game would be better for it.
