I share your approach. I would do a swim through, with an easy egress visible from the entrance. But I worry about what you describe, a buddy going off doing actual penetration. I think I would do as you did, and "peace, out" the buddy.
I dove the C-59 in La Paz in December. The guide did discuss swim-throughs on it, and said we could follow him or not. On the swim throughs, I followed. Some of them looked more like penetrations though, so I did not. I dont think he was doing a full course of the whole damn ship though, like the OP describes!! Thats pretty crazy.
If I buddy up I consider it a serious thing, like sticking to my word of honor. But when we have an agreement and the agreement is busted by the other party then my word of honor is then retracted. And the reason he was kicking up so much debris is that he had on free dive fins!
I just watched that movie about the cave rescue. Yeah, yeah, well, it is pretty good anyways. I am kinda like the grouchy British diver, I am not interested in dying. I have people who I am responsible to care for, like my wife. And I have told her she should not count on being a rich widower like her mom (or a poor one ).
The C53 is pretty mild, it does have tons of cutouts. But regardless, the guided dives I have done through it were penetrations though several sections with restrictions. I should not tell on myself but I like double hose regulators. Well, not sure I hit something or if I just tore the hose but inside that engine room area my regulator flooded out. So I went to my octopus, no big deal. But! Right equipment for the job. Course, that could happen on a rebreather but rebreather divers are set up with bailouts, so they have redundant options on board plus their buddy, OW divers generally do not. That was the same dive my S90 camera flooded. I was not a happy diver .
N