He bows to the Emperor because of two reasons: The Emperor is still on the side of the Republic (good) while the Jedi seem to have turned against the head of the Republic (bad). He needs Palp to save Padme, or so he thinks and thus must stop Windu from killing him (something against the Jedi code). I can see how very easily, those two things alone could confuse Anakin. Let's not even touch on the fact that when Skywalker walks in, Anakin hears him say "You are under arrest, my Lord". Yeah, I'd be confused as hell at this point. Turning to the Dark Side wouldn't be such an absolute, just an alignment with the only things you believe are still right at the time: Saving the Reupblic and stoping the war and saving the one you love.

As for Ewok over Greivous, come on. Greivous, while disposable, is atleast believable. If you take no umbrage with tiny forrest creatures bringing the Galactic F'NG Empire to it's knees. Something well armed, well funded Rebels couldn't do for 15 years, then I don't want to hear you complain about plot holes or lack of believability again.