I just set the rim on the horn of an anvil (so that the ID was supporting rather than the leading edge) and tapped the areas affected with the flat of a ball peen hammer. It did not take more than three or four light taps to bring the material down almost completely. The aluminum was not deformed greater than its thickness in any case, so it looks alright now...

Does anyone have experience with rim failure from such minor deformation? These are not expensive rims, but they are old and not easy to find. The idea of throwing one away just because the spoke holes were pulled out in a few places seems a pity.