Without knowing what is causing the discoloration - irritation vs injury or something unrelated to the penis pump - it's hard to say anything about the fix. You really should be seeing a doctor about this.
Stop using the pump and see if that helps. If you don't see improvement quickly, see your doctor.
If you are using it for penis enlargement, you should know they don't work to do that, no matter what they promise. They really only provide temporary relief for erectile dysfunction. If you are young and have ED, you really should see your doctor, as that can indicate a more serious problem, like heart disease.