i thought she stole her heart back?
of course i'm damaged, it's tattooed on my forehead isn't it?

Waller had her never under control, she was merely in the position to blackmail her for a short time.
It' like a savage beast on a chain. You can pull on the chain and drag it into a direction, but as soon as you turn the back on the beast it will turn on you.
You had to be on alert 24/7 but you can't.
A beast can be put in a cage so that one can rest, but Waller had no cage for the Enhchantress, only the chain (or here the heart to stab).
I guess she, the Enchantress, was set all the time to find her brother knowing that he could by-pass her "heart"-problem by sharing his power.
And when she had found him (and Waller was stupid enough to carry this information around her), she freed him, sent him out to feast and gain strength, and when he had gathered enough energy to feed them both she bolted - and because they were about to kill him.
But Waller was the problem in the first place.
If she hadn't been there, if she hadn't been allowed to use the Enchantress way before the meeting in the Pentagon, she never had had the chance to wake her up, or, indirectly, her brother.
It was pretty much clear that sooner or later the Entchantress would have found a way to slip off her grasps and persue her path of retaliation.
The weapon she created killed serveral hundread civilians of Midtown (at least), and many thousand soldiers on the destroyed carriers and other facilities.
But all this damage in human life and material that can only rbe blamed on Waller for She, Waller, had set her, Entchantress, in motion believing she could control her.
Waller also killed FBI officer because they had no clearencemore they could tell what she really had caused by her studies.
That she caused no good but only harm.
Ok, this is DC + bad writing - hence she got away with it.
But incompetent key-people like Waller are the actual problem.
People like her have to be taken out.
A god-complex combined with utter incompetence and a card blanch by the goverment is a package set for a desaster.
Ich bin kein ausgeklgelt Buch, ich bin ein Mensch mit seinem Widerspruch.
Conrad Ferdinand Meyer

It was not freeing her, it was killing her. But her brother could save her by sharing his energy, and I guess that was her plan from the beginning.
Ich bin kein ausgeklgelt Buch, ich bin ein Mensch mit seinem Widerspruch.
Conrad Ferdinand Meyer

No, the brother just saved her

I've been wondering the same thing. It seems that when Waller stabbed her heart, it actually ended up freeing her and being beneficial rather than detrimental.