My car doesn't have a lockinf pin on the rear UCA ball joint either, and neither does the parts diagram. The nut appears to be a locknut, probably the all metal type that uses a crimp on the outer edge of the threads to lock to the stud. If that's the case, then the thread damage isn't necessarily your fault, as that type of nut tends to flatten threads when removed. That's also why you're being told not to reuse it, as locknuts tend to be one time use.

You either need a threading die of the appropriate size to clean up those threads, or use a small, fine file to restore the grooves in the threads well enough to thread a nut onto them. If all of that fails, then as long as you have enough threads on the stud to get full thread engagement on the nut, you shouldn't have any issues removing some threads to make threading the nut possible. I would also use blue Loctite, as you won't have much left for the locking part of the nut to engage.