If you try to peen without proper setup like DeShivs is saying, you can also crack the scales.
As far as the scales coming loose because the heads have been filed off, that I couldn;t disagree with. So long as you expect that might be a likely result, you'll be ok. You'll need to remove the offending scale (or both, even better), get the old epoxy off, clean and/or etch the metal, and epoxy them back down. The pins (now headless) themselves will add glue "surface" when re-gluing the scales.
All of this work could be avoided by not messing witht he rivets, but if you want to remove the rivet heads, I think you certainly can without too much fuss. As I said, I'll do it to my EKA if the protruding rivets bother me and I won;t sweat the work involved.