Universal Solution
Many of the suggestions unfortunately do not work for all Markdown viewers/editors, for instance, the popular Markdown Viewer Chrome extension, but they do work with iA Writer.
What does seem to work across both of these popular programs (and might work for your particular application) is to use HTML comment blocks ('')
:
| | |
|-------------|-------------|
| Foo | Bar |
Like some of the earlier suggestions stated, this does add an empty header row in your Markdown viewer/editor. In iA Writer, it's aesthetically small enough that it doesn't get in my way too much.