The implication of deliberately allowing Emet to escape was written into the game script, though, which Yoshi-P also pointed out in his answer. Not that that makes things any better or not ill thought-out, of course. Even when it was being written into the game, I'm sure they were operating from a perspective of "wouldn't it be cool if all the pieces fell into place and everything Came Full Circle as part of the Grand Plan?" without thinking of the further implications.