You basically have 2 options to fix it correctly.
1. Remove the roof and roof panels to remove the cappings. You would then need to get them balsted to remove the rust, and repaint, or galvanize and repaint them.
2. LR has started offering a 1 piece side capping. The one you have is more than likely 2 pieces. The weld on the 2 piece one is where most of the rust starts. The 1 piece capping eliminates that particular problem. Also, these cappings are now available galvanized from the factory.
Either way, if you want it fixed correctly, the roof has to come off.
Hope this helps.