In LSF we actually RP escorting prisoners back to prison stations (Which give us some more RP to do, and gives them the chance of escaping). With a little bit of RP done by both parties, this can be done for both sides enjoying it.
Regarding those not complying pirates... why implement a command to automatically capture them? Let them do whatever they want, it's within RP for them to try to escape. And if you get a command to completely cut their engines off after shield are down, or similar things i've seen here, you would seriously limit their ability to roleplay at all. (Police sees a pirate, "Stop pirate, i saw you attacking that trader!" (Pirate: "Ehh? No, wait! We were only...") A full debbie round/torp/missile/SNAC + command and the pirate is inmobilized and unable to do anything.