Option 2, with some modifications, I think.
You have prisoners, a ship can pick them up with a "Load POWs" order, selecting which ones as necessary. The ship can then go to a body, and "create prison colony", and a small colony of that species is created, with the POWs. This colony will have significant unrest, and require a garrison to maintain order - if you don't maintain order, they'll rebel and become a hostile world.
Prison colonies can build the forced labour camps and mines, and not much else.
Ships carrying the same species of POW can offload them onto the prison colony.
Some method to distinguish between newly arrived and previously questioned POWs.
Also need a method to repatriate prisoners and friendly survivors to worlds of their own species. I've attached a pic of the prisoners in my War of the Worlds game - only the Martians were actually hostiles, the others are survivors that I've picked up, but have no means to repatriate.
Since I occupied Mars, I should be able to repatriate the Martian prisoners there (and this should cause some unrest).
NPRs (including raiders) should also have prison colonies for any POWs that they capture. And the player should be able to raid NPR prisons and liberate the prisoners, including any commanders.