True Resurrection can bring her back with her old original heart intact, it requires killing her first, that spell is a bit pricey, my 7 steps would be the most likely way to remove her engine.
1. Travel to the Material plane
2. ask rich boy Wyll to give up some of his dad's money,
3. Buy a scroll of True Resurrection,
4. Travel back to the Hells
5. Kill Karlach (it's only temporarily and she would be dead for a couple of minutes tops.)
6. Remove Infernal Engine (either by looting, passing a skill check or persauding Dammon to remove it)
7. Then use the scroll to cast True Resurrection on her corpse, (not only does it bring people back to life, it can also regenerate lost body parts and make undead creatures like Astarion into rejoining the land of the living, effectively curing him of vampirism)
1b. Get Gale killed
2b. Get the scroll of true ressurection he carries around as a precaution
3b. Use Withers instead to ressurect Gale.
