OK I had to read this a few times to understand the question, but the simple answer is that Primer is a paint and should be coming off with the simple green as well.
After scrubbing with a toothbrush and a touch of washing up liquid or sink cleanser (Cif) the models should be allowed to dry and then re-primed.
Process has worked for me on lots of occasions.
Sorry for not being more clear. Here are the steps I used.
1) Soak the plastic miniature (Necron Warriors in this case) in straight Simple Green. I'm using a plastic container and the Necrons are weighted down so they are completely submerged.
2) Allow to soak (in this case) for 7 days with agitation of the liquid each day.
3) Remove the miniature from the Simple Green and scrub gently with a toothbrush.
At this point all the paint except for the black primer is removed. When I scratch my finger nail over the mini's surface the black primer will come off but it will not come off using only the toothbrush. Scrubbing harder just makes the delicate miniature break or fall apart. It does not make any more primer come off.
At this point I decided to try two things in parallel. (1) I rinsed one of the miniatures well and allowed it to dry and see if the primer would harden as well. (2) I renewed the Simple Green and put the another back in the liquid.
The first one (1) dried but the primer lost a LOT of its adhesion. When I tried painting it again, some of the primer clumped up with the fresh coat of paint.
The second (2) got a small amount more of the primer off but not much.
I have decided to drop the Simple Green and go with PineSol. I have several of them soaking in a PineSol-water mix (about 70:30) and it seems to be working a little better. I let them soak for 24 hours and then removed and scrubbed them gently with a toothbrush. At this point I have very similar results to the Simple Green. All the paint came off but the primer is still there. After scrubbing each of them I put them back into the PineSol solution where they have sat for the past hour.