Ooo, another foaling thread, yay! Even though it was a mistake that your mare ended up bred, I'm confident you'll be a wonderful home for the baby. =)
I wouldn't allow this mare to be witchy about you touching her, seems like she needs some daily handling where you can rub her all over and get her tolerant of that. If not I'd be worried that once she foals, she'll either be just as witchy with the foal or won't allow you anywheres near it or her, if the foal needs assistance with nursing, etc. I consider the showing aggression with you handling any part of her body a sign that she doesn't quite trust you all the way or thinks she doesn't have to submit to your handling, although others might have a different opinion. Regardless of why she is doing that, she needs to at least build tolerance and learn to stand there quietly whether she wants to or not.
As far as her flipping out with the blanket, I think it had less to do with the blanket and more to do with the foal moving around in there, although the blanket likely aggrivated the situation. My mare had her first foal in 2012 and boy, was it an experience!
She is very sensitive to pressure of any sort and one day, she was going from a standstill to a trot and trotting a small distance away and stopping again. She would cock her head and looked as if she was looking at something behind her(on both sides), running from one of those bot flies as she would reach back and push at times. I of course, tried to come to her rescue and, armed with flyspray, went out to find this erksome bug. Turns out, she was running away from a part of her, lol.
I couldn't see her belly move from farther off, but that baby sure was having a party in there. My mare was very unsure of what was going on, as the foal (to my knowledge) has never moved with such vigor before. I reassured her and she got more quiet, but she never did look remotely comfortable with he would move so strongly again, lol. I only caught such HUGE movement a couple times after that. She would ignore small movement after a while =)
Anyways, what I was trying to get at was that your mare might have been experiencing the same thing, and if she is a maiden, might have panicked a bit about it and reacted in a very different way about it.
I would definitely have a smaller pen set up for them once the foal is born, some mommas don't want to be caught once they foal, lol. Also, with her being defensive with you, watch that she doesn't get aggressive about you being around the foal once its here. Keep us updated! What a story to come to such a wonderful family from a horrible situation and then surprise you guys with a baby!