A mate did that to my old jig. Similar thing, his router didn't have an electric brake and he pulled the router out before it had stopped spinning.
Repaired it with car body filler and it was fine. I did go a bit loopy at the time but in all honesty once filled it was as good as new.
In most circumstances car body filler is harder than most types of timber you would fill so you run the risk of damaging surrounding areas when sanding, but jigs are fairly hard so the filler sands down easier than the surround good edges of the jig, so you can get it nice a straight again.
I would suggest getting a pack of filling blades rather than use a filling knife, these are much more flexible so you have a greater deal of control when filling small areas. Less excess filler, less chance of causing more damage when sanding back.
You can get a set of filling blades for about £2 or the posh ones (wooden handle) are about £6
Filling Blades - UK