OK wait a minute guys...
Saying "I used a wire wheel" is no more specific than saying "I cut the tree down with a sharp pointy thing"... There are literally 1000's of types of wire wheel. I have some that have 0.003" dia. wires that you would feel comfortable using on your face to gently scratch an itch.
The point is, the problem is not using a wire wheel. The problem is a bad/over-agressive selection of wire wheel.
The rules are:
-thicker dia. wires = more aggressive
-shorter wires = more aggressive
-knotted/twisted wires = more aggressive
-having to push hard/bear down = both more aggressive and stupid, because it makes the wires bend, which means the sides (and not the tips) of the wires hit the work, which means they work much more slowly and wear out faster. Obviously, the more aggressive wheels can take more pressure, so on my most aggressive thick knotted wire wheels, I can bear down hard without this being a problem. You don't want to do this on your nice axe, though.
In general, skip using knotted/twisted wire wheels on machined surfaces and tools. They leave scratches in my experience. For something gentle, consider something with relatively short unknotted 0.006" wires as a starting point. You won't hurt much with those, but they're still enough to clean off oxidation. If you need to remove paint/heavier junk, then step up to 0.012" dia. wires and start out gentle. Again, this is just a rough idea/conservative starting point.
Weiler and C.S. Osborne make excellent wire wheels in the U.S.A. and will tell you all about it if you call them. They also print manuals that go into great detail about applications and selection. Or just take a look at some of the options:
http://www.weilercorp.com/power-brush-wheel-brushes
Ebay is a good place to find NOS ones. Double check the RPM limit of any wire wheel you use or you will spit wires, which is dangerous. And wear a face shield.
OR skip wire wheels and try 3M ROLOC/scotch brite discs. They will not risk marring your axes as much. These days, I mostly save wire wheels for parts that have odd, small cavities or shapes that are difficult to get to (wires can get into almost anything if you choose the right wire wheel).
**EDIT** Just noticed you asked for advice on how to remove the scratches. What tools do you have available? I would do ROLOC discs to smooth out the scratches if you have something that will take them. Or just wet sand with some emery cloth. If you post a pic of the scratches we can be more helpful.