Pegdown, as well as other Markdown parsers, translates code blocks to <pre><code>. This is the standard as per the Markdown specifications and both themes and tools (e.g. http://highlightjs.org/) rely on this syntax.
However, the doxia markdown module overrides this behaviour and uses "<div class="source"><pre>. It would be nice to revert the default behaviour to the standard. If there are use cases for such an alternative syntax, it could be provided as an option.