Yoda appears in a holocron during the game(somewhere in the Jedi Enclave sublevel), and it's logical because he is a thousand years old.
Also, I doesn't matter what alignment you are at the end of the game. If you are ls you get the lightside power, and if you are dark you get force crush.
Finally, I agree when it is said that the only fallen Jedi were Vrook and Atris in the game. Plus, Atris wasn't really a Jedi, because she was trying to restore the order on Telos, but wasn't padawaning.