There might be some other way, but for now what I had to do was to save the HTML generated from the Markdown conversion to a temporary file, then open that in Safari, have Safari select all and copy to the clipboard (copying an HTML object), then having Mail paste it – replacing the selected Markdown text. So, the service workflow takes the selected text, but does not itself replace the selection directly.

A PHP script and style file for generating rendered HTML from Markdown for pasting into mail messages. I use it instead of WYSIWYG editing in Rich Text mode because I'm so used to working in Markdown.

I run this from TextMate using the Mail Preview command:

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