Most of the rules we have here are to maintain the inrp nature of things. That one is to prevent a state where everyone and their brothers fly in caps. They have restrictions for a reason.
Want to allow caps to shoot pirating transports? Sure, but why not allow the same for pirates and smuggler-chasers? There's nothing actually 'prevents' them to do so... inrp. But that would result in a need of capital escorts, and where would that lead?
I say those rules are thought over well enough. If that disturbs your RP, imagine an Inter-Sirian convention of non-shooting transports in most circumstances, respected even by the most vicious bandits of space.