There are some instructions for doing this at the end of the README for highlighting-kate. Note that you'll have to recompile the library and pandoc, so this is only a good solution if you have a Haskell build environment set up and don't mind compiling pandoc from source.
In pandoc 1.12 (which I hope will be out this month), there will be an easy way to specify python "filters" that operate directly on the parsed document; so, for example, you could write a short filter that calls pygments to highlight code blocks.