A die might work, but you'd be cutting brand new threads at the very end, that might (or might not) corectly sync up with the good remaining threads further inboard... A better option might be to use a (corect size) thread file, like these:
http://www.google.com/search?sourceid=navclient&ie=UTF-8&rlz=1T4DMUS_enUS221US222&q=Thread+file
can I try to cut some of the end off? or will that damage more threads...
Was it damaged from cross threading?
How far in are the threads actualy damaged?
If you deside to cut... Look at your axles good side to see how much of the threads/axle stick on through
past the nut. That will tell you how much of the damaged sides threads you could cut off if necessary.
As far as actualy cutting it goes, A 4" Mikita type grinder (with the corect metal cutting type disks) would probably do a nice clean job.
Another more ghetto cutting method would be blocking the karts rear end
safely up off the ground, then running the engine set to fast idle, that would be turning the axle, while you carefully held a good hack saw, that would be cleanly cutting only the damaged portion off.
After cutting, you might find your (new???) axle nut still wont easly start and thread on. You might find you have to just very lightly file the very outer edge of the the axles threads to get your new nut to corectly start without stripping.
Good luck man... I'm pullin for ya.