You are absolutely correct that he had no authority to perform modifications to a critical public service, and that his actions bordered on reckless and negligent and that his response to the captain's accusations was cringe-worthy as well as indicative of the ignorance of his actions, but I think it stands to reason that the captain could have handled the situation more diplomatically.

Granted, I would probably get into a shouting match with Clemans for what he did (and I'm just another developer), but that hardly justifies barring him from entering the premises until further notice.

Clemans' actions can be chalked up to youthful ignorance and exuberance, whereas the captain has no excuse. He is the central source of truth and the ultimate arbiter in the situation, he should know better than to react so aggressively to one of his own staff members.