Two choices, as I see it.

1- Drill the hole out and tap it up to the next screw size and buy a new screw to fit.

2. Try to clean it up as it is with the same size tap...although it may be too far gone.

I'd opt for Number one...if it's possible. But I havent seen your trolling motor....so I'm guessing here. One of the pros may have an answer....like inserting a helicoil if there is enough depth to work with.
+1 Or if you don't adjust and usually run it in one depth postion you could put a hose clamp on the shaft above the bracket or better yet get a split collar. One like that is on a foot controlled motor that holds the two shafts together. I don't know if you can get them at an autoparts store or not. If not either a trolling motor shop or they might be cheaper at a place like Grainger or McMaster-Carr.