Without the Lady's cards being properly tabled, there is no way the pot should be awarded to her, in my opinion.
If her hand were properly exposed, face up for all to see, that is a different situation. The rules clearly state that a winning hand can not be killed provided the player is in for all bets and the hand was properly tabled but mistakenly mucked by the dealer.
Did the woman know she had a flush? Aparently not, otherwise she would have announced a flush instead of saying, "Two pair."
The dealer also is not completely at fault. The dealer will assist the players in reading the proper hand, but, the ultimate responsibility is with the player to protect their hand before it hits the muck.
I do agree that you should NEVER go into the muck in poker. Muck cards are dead, and when properly mucked, they are mixed into the muck in such a fashion that it can not be determined who originally possess which cards.
Mucked cards in black jack are stacked in order, so each hand can be examined, but in poker, they are not!
So, if the information you gave was accurate, in my opinion, the mucked hand had to be properly tabled in order to award her the pot.
If the decision were based on players, looking into her hand before she mucked them, without putting them face up on the table.
The pot should have been yours.
I hope I've explained your situation so it can help you in the future.