You're right, it could be that he didn't want to hurt his father in the process, and eventually "save" him.
But why didn't he want to kill the Emperor, though? I don't get it. He was trained just so that he could defeat him:
Only a fully trained Jedi Knight with the Force as his ally will conquer Vader and his Emperor.
Yoda says he knows everything he needs. If he can't defeat the Emperor because he's afraid he's not ready yet, then his masters have failed :D