MarkitUp (beta) is a wordpress plugin which allows you to use Markdown on your site without breaking existing content
The WordPress default editor will be used
Currently each author has to manually enable it in their settings, so there is nothing to worry about
Do let me know on Twitter http://twitter.com/kennydude
This is on a site-wide basis and can be enabled by going to Settings -> Writing and there is a "MarkItUp" section.