Hey!
I totally get why this is confusing, but a lot of Lark's story is instead of fighting his battles for him, letting him grow and break away from Isadora's abuse on his own! There is a lot of parallels between Lark and Isadora's relationship and then a toxic/abusive relationship. A big thing when we were writing was that if this was a real scenario, and not paranormal, if you yell at someone to leave or push them before they're ready to do it own their own it can often times make things worse!
Another thing is standing up directly to Isadora (the abuser in this case) is only causing her to double down harder and she would be attempting to paint MC, who is a stranger that just got stuck there one night, as a bad person who doesn't know them. Overall Isadora is super controlling over Lark in virtually every way, down to borderline grooming behavior to make him the perfect companion for her
Hope that makes a little more sense!