Sometimes destiny does not want someone to get what he actually deserve. We know from history that a certain austrian whas the target of many people that want him away but nothing worked. Maybe the protagonist saw with how much he got away despite he should actually get fired to the moon so he decided to just let Karma do it's work in peace. I mean if you want to complain about the protagonist not stepping in, start at their boss. He even once said, that Bauer should actually be fired a longt time ago but it finally is the day when it happened after the thing with the corpses and the necromancer but he is still there.
So either his chef does not want to do anything either despite he is giving the opposite impression or Klaus Bauer is really getting protected by a higher power, be it earthly or metaphysical, and so the people arround him know for better to not interfere as it would make thinks worse.