I've been looking recently at using criticmarkup together with markdown, and it seems really promising. Editorial on the iPad and both Multimarkdown Composer and Marked2 on OS X support displaying criticmarkup within your editor.
It would be nice to have equally convenient ways to automate accepting or rejecting suggested additions, deletions or changes, but the OS X system services in the criticmarkup site's toolkit did not work correctly when I installed them, so I'm gisting a couple of perl scripts that accept or reject criticmarkup in standard input.
- gist to accept criticmarkup
- gist to reject criticmarkup
It shouldn't be a big job to turn those into system services. I've never used OS X's Automator, but maybe that would make a good afternoon project...?