I don't think you can refit fighters, unfortunately.
Apparently you're supposed to be able to put a fighter in a hangar, then use the Damage Control to draw from the mothership's maintenance supplies to effect repairs. This doesn't apply to armor damage, though. I've never done this though, and it only works with spaceborne hangars (so not in PDC fighter bases)
You can scrap them from the Industry tab of the Economics window; press the 'Stockpiles' button, above and to the right of the Industrial Allocation form.