Right. I know how this can be done, but it isn't pretty. You will first have to either make a new structure exactly the same as the refinery, with it being capturable, or just edit the existing one. However, if you edit the existing ones it will be applied to them all, even the ones built by the player. I don't have time to write out a tutorial, but after Sins Plus 1.3 is released and working, I will happily write one for you. Can you wait a few days?

If you can, have a good look at how the GalaxyScenarioDef file works, and get accustomed to it. It will help you massively when I come to write this tutorial.

Basically, you will be creating a refinery which will belong to the Pirates or Militia. They shouldn't be able to use it, so it won't effect them. However, you will be giving it the Passive ability to be 'Capturable', and this should allow it to be captured like the neutral asteroids. You will be adding it through the GalaxyScenarioDef (GSD) file, and not the planet files themselves, as I don't think you can do it that way. It will have exactly the same effect, just you will be editing one big file, rather than all the little planet files. This is why having a look at the workings of the GSD file will help you infinitely, when I come to do the tutorial.