First off, let me say that leaderboard distortions have never bothered me overmuch, and I wouldn't have complained had Doug chosen to make no changes at all. That said, if we are going to try to remove distortions from the leaderboard, I think certain things are quite clear:
Requiring Colony should definitely not count. It is a huge win-rate advantage to only playing Colony games, get really good at them, and play lots of them against opposition who are not Colony specialists. Back before requirements were displayed to your opponent, almost all of the top slots on the leaderboard were Colony specialists (based on their Popular Buys data)
As far as allowing some small number of prohibitions, well, I don't see why anyone who wants to prohibit even one card they're not good at should feel entitled to have their mildly-rigged games rated equally with completely un-rigged games. If you need some prohibitions to have fun playing, by all means, make some prohibitions and have fun! But if you genuinely want to compare your skill with others via mathematical ratings, then leave your prohibitions at the door, because rigged games make mathematical comparisons meaningless.
Removing games with any requirements/prohibitions from the ratings is basically the minimum requirement for producing meaningful ratings. A big step in the right direction, here. Better still would be to have a "rated game" type that only reveals the board after all players have accepted the game, and only count those games. But that's a bit more implementation work, of course.