if you cut off the remaining nubs then you will have to re drill and tap new holes, that will be a big PITA, you will need to remove those nub studs, use PB Blaster or the like and a pair of vice grips and work at it, then you can clean them up and coat with anti seize....
as for refinishing... well the best is to remove the bar, media blast and powder coat but for the shadetree body shop remove just the affected area with the grinder and repaint that area, as for a matching paint try some diffferent brands but I have found POR-15 to work the best at sealing up steel.... start in a small area and see what the results are -Andy