If you don't want Mint to get that $3.41, just update Banshee from their PPA -- that should remove Mint's (or Canonical's) affiliate code, right?
I feel like Banshee should get the proceeds from these sales to keep Banshee in active development -- Mint and Canonical should feel this way, too. Why wouldn't they want to support their upstream components? In theory, they could burn through all the good media players they might integrate into their distributions, if this affiliate pocket change "theft" caused them to cease development.