Sally is always going against Dr. Finkelstein.
She's tired of being locked away and held captive at her creator's house.
She honestly should have known not to trust the mutant duck that kept her captive.
Instead of locking her away like usual, the doctor decides that he's had enough.
He's already in the process of creating a new wife, he has no need to keep Sally around anymore.
He could do the easy and nice thing and just let her leave, but the Dr. doesn't want that.
Sally would have stayed alive if only she kept struggling and not go back to the Dr.