screws are available that can be used to fill the holes and not have them look hacked upon.
Sometimes a hole can be filled by carefully threading some rod, or using a close fitting screw, cutting it off a bit above flush, peening it over a bit to swell it in place, then finishing the area. It can look really well done (almost invisible) or it can stand out like a sore thumb, depending on a bunch of different things, like if the guy doing it was holding his lips right at the time, or if he sacrificed the correct color of chicken under the proper phase of the moon...
use the blanking screws. They can be removed, and the sights replaced, if you desire, at a later date, and the look quite correct when in place.
Cheap too.
Got a brownell's catalog? You should get one. Lot's of good ideas there!
Cheers
trev