First off, thank you for making this fantastic plugin.
Could I just make one small request for the next version of this plugin? When you enqueue prettify could you use 'prettify' as the handle rather than 'markdown_pretty' which you are using now? The reason is that I am using a theme that has prettify support built in, so enabling prettify support in your plugin causes the prettify script to get loaded twice. I think this could be an issue for other people who use similar themes or plugins which also reference this library. If we all used a common handle (my suggestion is 'prettify'), WordPress would only include it once.