Well it sounds like they have pretty solid reasons for their rules.Yeah you can go on their charter and just swim off by yourself. And you won't ever go on their charter again.
They're pretty anal around here about the buddy system. They say it's due to their insurance requirement but I suspect it's probably more about the bad publicity of being the dive shop on the news that had a diver drown. I can't blame them for that. Nobody wants to be the boat who calls the Coast Guard to tell them you're bringing a dead diver back to the dock.