Bernie thinks, "I felt lucky. To have been given the choice, the ability to go back in time and unmake my mistakes. Lucky to be in control of my body, self-governing and whole. It was what we all wanted. To choose our own freedom, to choose our own pain."
I don't know if it's possible to "unmake mistakes" - particularly those that harm other people.
If "choosing our own freedom" means escaping consequences, then Brid also seemed able to do that after her IRA venture by fleeing to the U.S. and taking on an assumed name. However, she never could escape the guilt she felt over both that act and her belief that she caused her sister's death by allowing her to go out that night. Even confession couldn't erase the consequences. So - no "freedom" there.
Aoife - and Sean, similarly, couldn't erase the "mistake" of getting pregnant and being subsequently stuck in a marriage and life they both hated.
Since the consequences for Brid and Aoife and Sean also extended to harming their children, I guess one of the reasons we are asked to see Bernie's abortion in the light of "wholeness" and "freedom" is that - since she, like them - was in a bad place emotionally, her decision to end her pregnancy was actually better for her baby than a future life of potential harm. Or, given her emotional state, it was better to sacrifice one life than two (and potentially more if the dysfunctional family cycle continued.)