Citations of the scholarly literature are an essential part of scholarly texts and therefore have to be supported by scholarly markdown. Both the Pandoc and Multimarkdown flavors of markdown support citations, using a bibtex file that contains citations, placeholders for citekeys – [@smith04] for Pandoc and [#smith04] for Multimarkdown – and the Citation Style Language for citation formatting (Pandoc). A very reasonable approach would therefore be to use this functionality, with a preference for Pandoc because of the Citation Style Language support. All reference managers can export to the bibtex format, and some of them (e.g. Papers) make it very easy to copy and paste citekeys.