My guess is that it would depend on your daughter's age and just how busy they are in there. There were several signs stating that the microwave was just for bottles and baby food.
From what I have read, it seems like Disney tries to be very accomodating to guests with special needs so maybe if you ask at City Hall (?) and explain your situation someone could tell you where there is a microwave you could use. Also, someone over at the disABILITES board might have a better answer for you so you might want to try asking over there too.