Handicapped match play? You'd have to figure out some way to rank the hardest holes on the course. Ball golfers have explained how to do this to me.
In ball golf the indiviual handicap of a hole is based on average score above or below par for that hole.
So where a par five might be 600 yards, if the hole is all down hill, easily reachable in two by most golfers
and averages 4.3 strokes. Take this compaired to a par 3 the is 175 yards, all the carry is over water and it is surrounded by sand traps, the average score here is 3.75. The Par 3 is obviously going to be handicapped lower (harder). Ball courses also break the handicap up by front and back nine, if the #1 handicap is on the back nine, then the back is odds, the front even numbers. I believe this is done so if you are giving someone four strokes they aren't all stacked on the same side of the card.
I would think you have to keep league and maybe tournament scores on all holes individually, and likely for an entire season. this would allow enough data to develop a fairly reflective handicap of a course. There is also the issue of moving the pin. While ball golf moves the cup, usually weekly, the distance doesn't vary as much as it does with disc golf, in general. It would be pretty darn cool to be able to play leagues, tourneys etc with a handicap but I think what you have going this summer might be the best method?