This came up in a game we played just a few hours ago. We house-ruled it that because the villains' defeat actions removed the token NOT the Heroes' actions, it is valid to remove it.
Defeating a villain is an action the Heroes take during their action phase of the turn, and thus the rewards gained are gained by the heroes. So, the dark mark being removed is always removed by the hero, and therefore would be blocked.
Similar to gaining 1 heart. The villains don't gain a heart.