vimwiki does support markdown out of the box as of v2.0, though you have to set an option for it...
let g:vimwiki_list = [{'path': '~/my_site/', \ 'syntax': 'markdown', 'ext': '.md'}]
let g:vimwiki_list = [{'path': '~/my_site/', \ 'syntax': 'markdown', 'ext': '.md'}]
(Now if only I could figure out how to get Vim Touch on Android to correctly format vimwiki pages...)