I think pickup choice matters alot for industrial. As darkandrew says, you want something with cut, and also able to handle effects without falling apart.
Rebel Yells do have alot of cut, but they sound too friendly I think for this job. You certainly want something with a ceramic magnet and grinding. It depends on the amp you use for the exact choice, but I would also think about the Cold Sweat.
For me Ministry and NIN have different tones. Old Ministry is more like a trash tone, and I think the Cold Sweats would be good for that, whilst also being able to do a more alt sounding NIN tone.