This has been discussed a bit over at Board Game Geek, it's actually an error in the rule book. The troll would absolutely deal his counter attack damage in the scrum, unless a unit had a swift attack that took him out of melee before his turn to strike came up.
Hope this helps.
BTW: this game has a fairly active following on BGG:
http://boardgamegeek.com/boardgame/146418/warhammer-diskwars
You may want to check it out if you're looking for faster answers to your questions or other details on this awesome little game.