I'm not going to make the prisoner issue over-complex. When a ship surrenders, it becomes your ship with an overhaul factor of 0.01. This is the same as capturing it via boarding combat. You can scrap it, refit it, etc..
For the crew, I don't have any specific code yet but it would make sense to treat them in the same way as rescuing alien life pod survivors. You gain intel and the survivors become POWs, which you can drop off at a colony. In this case, they would be POWs on what was their own ship and you will need to add a crew. I'll probably create a small 'prize crew' for free and you will need to get the ship to a colony to take on a full crew.
There is no code for POWs at the moment beyond tracking their location, so I will look at that as part of diplomacy.