theres no way impel down can be justified, and unless it was anime only magellan literally killed a bunch of prisoners just because they were being loud and annoying
It's show multiple times that ID is not only a prison but a way to execute prisoners in the most painful way possible. Part of Magellan duties is killing scum and deliver proper punishment. He would only get in trouble if he went excessive on their asses, like the other warden.
Special note for the fact that level 6 prisoners are only alive because of mercy (in the sense that the WG wants them to pay for their crimes and death is a release) and not because they could be released later. They were erased from history for a reason.
Look again to the situation by the perspective of a WG employee: the prisoners started to get rowdy, Magellan warned that it would have consequences if they continued, they didn't stop and Magellan decided that they aren't worth of the trouble. Not only this serves as a way to keep his authority but solves the issue immediately. There's a reason why people don't cross Magellan.
Shiryu of the Rain was the opposite. He was considered a psycho because he killed without rime or reason and went overbord, so he was given a time out to calm down.