Markdown doesn't use triple backtics for code blocks, but instead code blocks should be separated by a blank line and indented by 4 or more spaces.
Github-flavoured markdown (which isn't strictly speaking markdown) implements triple backtics. While it's possible to implement it, GFM breaks with markdown in a number of ways so the plug-in wouldn't be true to what it says it'll do or it'll have some weird hybrid of markdown and GFM markdown :). (Reminds me somewhat of http://xkcd.com/927/ :) ).
I'm open to pull requests which add an option which essentially replaces markdown with GFM, but I'm afraid it's something I don't have the time for currently.
But you can use Highlight.js with markdown, Marcin has created this plug-in: https://github.com/mczenko/wp-markdown-code-highlighting-options. Someone has also this plug-in which seems to do exactly the same thing: http://wordpress.org/plugins/wp-markdown-syntax-sugar/. Both it appears allows you to use wp-markdown, with wp-highlight.js.
... I should add a link to those plug-ins as a couple of times people have asked about wp-highlight.js support.