I did this a while back. Yes, you can drill the rivets out but be careful because the timing cover is softer than it looks--easily chewed up by a drill bit.
Backing up a bit--I bought a new "Medallion" timing cover for my FXR2, to match the Medallion trim used in many other places. It came with a self-tapping screw, two chrome allen heads, an allen wrench, and the cover itself. The holes on the medallion cover are at 12 and 6. If I remember correctly the rivets are at 3 and 9. After drilling the rivets out, you find a cover plate that is screwed to the housing. This plate has two holes at 12 and 6 that are not threaded. Using a phillips screwdriver and the self-tappping screw provided, tap the two existing holes and use the two allen head screws (suggest a touch of loctite) to attach the new timing cover.
I mention damaging the original cover because the HD instructions with the medallion cover say what size drill bit to use (I forget the size) but I would say to use a smaller one. I followed the instructions and damaged the original cover.
So, yes, you can drill out the rivets and re-attach it with screws.