I would do one of two things (or maybe a combination?):
It doesn't look like the tab which holds the rod does anything structurally. Either remove it (green line) or cut it back (maroon curve). In either case, this would leave the rod hanging free where it's not connecting with the body panel. Make sure you keep the hole at the top where you have it strung through right now so you'll still have a mounting point for the rod. To reconnect the rod, get some stainless steel wire to tie it up. This will ensure it doesn't rust again. Should never have to worry about it afterward.
Something else you could try is, cutting the area back (like I was suggesting above). You'll want to go to a hardware store and buy a stainless steel washer which is about the right size to hold the rod but still have some slop around it. Cut a notch in the washer so it will go over the rod, then weld the washer onto the tail gate housing to hold the rod in place.
In either case, get something like POR15 and coat anything which looks like it could rust except the rod itself. Since it is on the inside of the tail gate, you should have to look at any ugly stuff. After this you should never have to worry about it rusting again and I would think it would last for what ever life is left in your truck.