I wanted the same thing for the same reason (creating a website using Hakyll) and I found the "problem": the CSL file.
Pandoc, in fact, does this job perfectly and the solution provided by MacFarlane is correct, but it lacks explanation on the rule of the CSL file—it is what defines if you are going to have a numbered reference in the middle text with a list of publications in the end or not.
Julien Tanguy has created a CSL style that puts the publication simplied information from BibTeX in the place where the reference is cited, derived from Chicago style. Certainly you can use it (it is licensed under Creative Commons Attribution-Share Alike 3.0) but you can also create yours.
So, now (a long time after you've posted the question), I hope you have the complete answer.