How about using the 1/8" "one-toe-foot" or a 1/4" foot and sewing with the other color right next to the stitching you've already done - both stitchings would then have both colors & look like it was supposed to be that way.
OR use a twin needle & follow the existing stitching to add the secondary color, then continuing with both colors for the rest of the quilting.
As long as you're considering restitching, AFTER you've ripped out the 'wrong' stitching (and your hair...), just adding the other lines of stitching would be less work and less exasperating, plus no 'holes' to hope won't be noticeable.