As a CoC player, I just avoid Nurgle's Rot. There's not a very strong incentive to purchase the gift for my tainted ones, and if my Carnival Master rolls the spell everyone in the group agrees that it's OK to re-roll for a different spell. I haven't played with a cart in a long time, but I think we just dropped it from the cart - it's still really good even without the rot.
The thing is, Nurgle's Rot doesn't directly assist the CoC player - it doesn't get him any more gold, it doesn't get the warrior who caused it any more xp, all it does is probably, eventually, kill off an opponent (and weaken him for subsequent battles). Ganging up on an enemy is a much more efficient way of killing him off than waiting around for him to fail those toughness tests.
Plus, as your group has apparently already experienced, it just generates ill-will towards the warband and whoever's playing them - no fun for anyone.