I have not yet contacted them. Unless I am mistaken, since they registered the subreddits, they will always be moderators, and hence the conflict of interest cannot be completely removed.
Going forward, the best thing to do is be very active on
the subreddit registered by the Counterparty team, to, at least minimize the ambiguity as to which subreddit is "the Counterparty subreddit".
It is possible to request subreddits when they are abandoned. The core rule to determine that seems quite stringent, though maybe there could be some admin discretion involved in the final decision.
Subreddits aren't considered "abandoned" if any mod has been active anywhere on reddit in the past 60 days. Keep in mind that "activity" isn't limited to posting and commenting.
Requests are made here:
http://www.reddit.com/r/redditrequest See the sidebar for more info.