Assuming you have already created your index.markdownfile for replacement index.html, you can modify site.hsit to look like this:
getResourceBody
>>= applyAsTemplate indexCtx
>>= return . renderPandoc
>>= loadAndApplyTemplate "templates/default.html" indexCtx
>>= relativizeUrls
The new line - the third, >>= return . renderPandoc.
Pandoc HTML, HTML, Pandoc .
, Hakyll: https://groups.google.com/forum/#!topic/hakyll/ooMEwuiQZ24