On my most recent rewatch, I noticed something...
Keller's abduction of Alex actually saved his daughter and her friend.
It started a chain of events that led to the ultimate resolution.
Think about it: Keller kidnaps Alex, Mrs. Jones grows lonely and lets Anna and Joy out of the pit - in turn giving Joy the chance to escape.
Furthermore, Keller kidnapping Alex is the reason Loki went over to Mrs. Jones’ at the time that he did - when Anna was about to be lethally injected and he being able to save her.
Plus, everything that followed resulted in Alex being identified as Barry and reunited with his family.
So one might say Keller's actions were morbidly necessary.