My professor told me she went through the same thing while she was going through an Experimental PhD program at a reputable university. She ended up changing advisors, and pretty well told the woman that she was working under that it just wasn't working out, and she needed a change of supervision. Would this be an option for you if transfering looks like a pain? Yeah it may be awkward for a while, but one you are away from her, she looses the control anyways. In my opinion you have every right to look for someone else to wrok with! And I would hope that the head of the program would agree.
On the other hand, my professors have also always told me that transfering during a Clinical PhD program is not unheard of, and that sometimes life happens and you have no choice!
Good luck!!