A lot of people have been through this and your options have no definitive answer.
For a little .22 pump, maybe you don't need a scope. Lotta people don't. But apparently someone did.
So your task is to fill those holes like they never existed and I hate to break this to you, that's never gonna happen. It will always leave a mark and a trace unless you get really lucky.
The screws will be of a different metallurgy than the receiver, which is slightly different than the barrel. If you were trying to do a full-up, hot-dip reblue on this thing, you'd probably be fighting it to get a good match. So the off-color pimples from the screws, no matter how well ground and finished, will probably always be there. Restoring this to exactly collector grade original is basically off-the-table, though you might get close.
Alternately, just buy some plug screws and tighten them in. Who knows? Maybe someday you'll change your mind about a scope. Besides, maybe the next guy will think of it as a "feature" and be grateful for the work already done.