Although I don't mind Arsen getting in trouble for allowing his fellow soldiers to die, it sort of doesn't seem likely. if anything, soldiers get in trouble for showing mercy and ignoring the objective, which in this case should be the prevention of Gundam theft. It seems unlikely that he'd get blamed for deaths that are technically caused by the enemy. Though he could prevent their deaths, failing to do so does not technically make him responsible for their deaths. The availability and credibility of witnesses to this act of questionably intentional negligence is also difficult to obtain. Who is around and in a sound enough state of mind to say, "Hey, he let those guys die," that Arsen cannot just pass off as "I didn't mean to", I didn't know" or "it was an accident".
Again, I don't really mind if Arsen does get in trouble for the sake of dramatic tension, and maybe OMNI is full of arseholes trying to get the controversial extended program in trouble. Arsen probably wouldn't mind even if he did get in trouble unless his punishment was gamma-glipheptin withdrawal.