About 15 years ago I salvaged the 30' x 60' metal roofing and trusses on an old fire station that we were taking down for replacemtn. I then built my woodshop to that size in order to reuse the roofing. While I DID use the trusses, I finally decided it was NOT worth reusing the metal roofing. I made that decision NOT becasue the roofing was in bad condition (it was decent grade architectural metal roofing in decent condition, but I did NOT want to go back and make sure that every single nail hole would be refilled and then miss one or two and have to go up and seal them off again. Went with the new metal roof and have not looked back...used the old pieces to keep the lumber dry in the lumber yard.
That being said, in your case, it mostly depends on where/how it is leaking now. Also, the problem might well be pulling the nails without further damaging the roofing...otherwise noting wrong with the idea.