So basically if we can get a sort of emp weapon to deactivate their shields then they're killable.
Keep the guy, at least for now. If we hole him up in the brig and lock down his ship he probably can't do much.
We just need to send him the message that we aren't gonna kill him and he'll probably be willing to negotiate.
When we leave, don't tractor him into our loading bay because he could do significant damage with his arsenal onboard. Keep him close to the ship, though, to shield him from attack, and close enough to quickly bring him in if necessary. Then head over to the SE starport.