I personally wouldn't do it, not solely because of the ages of the children but because of all the things that can happen in a hotel. Now, I'm 22 and have no children, but I am big on precautions (not what you typically think of a recent college grad, but oh well, LOL), especially after volunteering for quite awhile at a preschool. I doubt any of us really think of seedy people hanging out in Disney resort hallways waiting to break in rooms or trick people into letting them in, but you never know what might happen. That being said, if you do go ahead with your original idea, I'd strongly suggest going over how to lock the door (I believe there's a deadbolt and a swinging metal type lock) with her (and the obvious one of don't open the door to strangers).
The fact that almost all of the rooms have balconies should be something you should think about as well; no matter what age, it's easy to go out there and get dizzy when looking over the rail (especially when added to the heat), and that can (obviously) be very dangerous. That happened to me this last trip; I got really dizzy and had to sit down quickly. So, again, if you do go with your idea, making the balcony off-limits is probably a wise idea.
I agree with other posters' suggestions that going out on the balcony would be a nice idea or hire an in-room babysitter (if that's only do-able for the 2 year old, perhaps use the kids club for the 12 year old?). Better safe than sorry, imo.