We arent supposed to get it.
There isnt some cut and dried playbook for what Ollie's doing. Merlin is his sister and dead best friend's dad, he didnt kill a woman Ollie was close to, who was the sister of another woman he was close to. And yet he almost destroyed the city and has caused no end of grief for Ollie. LOTS of emotional shit right there.
He made a gut choice.
He may very well come to regret it.