What were they going to do with Babe after the torture?
It seemed to me that once it dawned on Szell that Babe knew nothing, Babe was expendable. He was indeed being shot at later on by Szell and the henchmen at the house. But at the same time, if he really was expendable, why not just kill him then and there in the place where he's been tortured, or Janeway could quite easily have pulled his gun out during the foot chase when he was right behind him.
Turns out Janeway was pretty inept at his job for someone who I'm guessing has more experience at this kind of thing.