This is quite an obscure combination, I guess; and maybe Meta-Description does not make sense for SEO at all (anymore). The latter point came to my mind just now
Still, I ran into the following situation: The Metadesc plugin extracts the first 120 characters from the entry body (actually, from $GLOBALS['entry'][0]['body'] - d'oh) and writes them to the meta-tag. Of course, the global array still contains my Markdown code.
Markdown code in the meta description looks pretty awful. I noticed when I wanted to post my entry to Google+ because G+ reads the meta description from a given page.
I fixed it for me by adding the frontend_header event to the Markdown plugin and exchanging $GLOBALS['entry'][0]['body'] with "clean" content. I'm not sure if this might break anything for other plugins?
Actually, changing anything in the $GLOBALS array appears to me as pretty stupid in retrospect. It's probably more reasonable to disable the Metadesc plugin in any case.
I haven't committed anything yet. Sooo .. thanks for listening anyway