I'm not sure I understand where you are going with your question, but I'll give it a shot.
MVC is an architectural pattern which in its essence means keeping the data model, the controller and the UI loosely coupled as much as possible.
You are trying to boil it down to the technological level, and it's not really making any sense. You can do proper MVC with a good framework. Just to make things clear, plain-vanilla PHP does not give you good MVC support. A good framework, such as CakePHP or CodeIgniter - will.
JS is just a nice way to enrich the client-side experience. Meaning that unless you are doing server-side JS, the only place you will have JS is in the view itself. AJAX requests have nothing to do with MVC, per-se. Neither does data persistence. Unless you are implementing your own controller (and you better have a damn good reason to do so yourself), you shouldn't be worried about its internal logic.
Bottom line, if you want to do proper MVC, use a proper framework, and all will fall into place.