So Lucian realized(or started to realize) that killing Ygerna wasn't the brightest idea. She was evil, lucian was good, but executing Ygerna pushed Damian into becoming big bad guy.
Instead Zandalor could imprisone her in some sort of magic prison (like Lucian was imprisoned) and try to explain to Damian truth.
But past deed cannot be undone, and if Ygerna would be alive and Damian would remain good guy then there would't be divinity 2 to play, so it's alright
