During WikiSym, we (Christoph Sauer, Janne Jalkanen, Ward Cunningham and I) held a five-hour workshop where we agreed on a new common wiki markup based on looking at the markup of popular wikis as well as deciding what would be intuitive. Our conclusion was not to replace wiki markup, but rather to provide an alternative way to edit wikis, so that visitors of a new wiki engine will feel more welcome. Several wiki engines have agreed to jump on board (including MediaWiki and the Ward's original WikiWikiWeb).
Although we do not say how to implement Creole for a particular wiki engine, two possibilities would be to have a separate edit button, using placeholders to hide advanced native wiki markup from users or if possible to have a mixed edit where users could use Creole as well as native markup which would then be translated to the native markup.
We have set up the WikiCreole wiki (www.wikicreole.org) to continue the discussion and work. We would be interested to know what you think and to hear from you if you would also like to add Creole support to your wiki.
Starting points: - http://www.wikicreole.org/ - http://www.wikicreole.org/wiki/AllMarkup - http://www.wikicreole.org/wiki/Engines
Best wishes, Chuck