I am quite sure that the markdown-plugin is not adding the nofollow but the q2a core. If you want to change the order, see these files:
1. qa-app-format.php: functions qa_html_convert_urls + qa_url_to_html_link, adding it as <a href="..." rel="nofollow">
2. qa-htmLawed.php:
line 515: // if(!preg_match('`\bnofollow\b`i', $a['rel'])){$a['rel'] .= ' nofollow';}
line 518: else{ //eetv (no nofollow): $a['rel'] = 'nofollow';