I don't think car makers install emblems by drilling holes anymore. I think your idea would be the easiest to do. Buy new GT badges, remove the 289 badges (WTH was that guy thinking??!!), then place the new GT badges in a position that covers the holes that guy drilled into the fender.
You should be able to remove the old GT badges with fishing string. If you have a heat gun, you might want to warm it up a bit to get the adhesive gooey first. Then take some goo gone to remove the residue, then wash with soap and water before installing the new GT badges.