You're mistaken. This converts the markdown HTML and sends an HTML e-mail. There wouldn't be much point if the receiver required a plugin they're unlikely to have. http://markdown-here.com/features.html
Usually Mail clients send mails as multipart/alternative with both a text/html and text/plain.
It makes sense to keep the entered markdown as the text/plain part. But if this looks ugly, then the plain text view won't be as pleasant.
PS.: I hate all companies that think their newsletter only needs text/html, and put a "Please read me with an HTML-compatible mail client" as text/plain.
