The comments over at the umpire ejections blog insist Wakefield stepped towards the plate. I put together a photo with two screen grabs that show his step was much more towards third than home, and they still insist on balk.
Obviously I don't know what Francona said to Hernandez, but the ejection seemed way too quick. Hernandez held out his hand as if to say, "Don't come out here" (much like West often does). It seems to me the interpretation that you can't argue balks doesn't preclude a manager for asking for clarification on what the balk was.