The Main Dining Room does a great job dealing with that sort of thing. There's a real advantage to having the same waiters every night that know your situation. They'll take your Sister's order for dinner the day before so they can have everything prepared according to her needs.
We have had good luck in the Windjammer as well, but it's a little tougher because they don't have that same advance preparation time. If you speak to someone there, they'll probably grab a Chef to talk to you about her dietary requirements.