It seems that both formats support tables, though they are completely different formats. GitHub Markdown supports embedding the relevant subset of HTML, though I'm not clear how, or if, this is possible in Hackage's markdown.
If this isn't possible, disabling the display of a region of markdown in the readme of the generated Hackage markdown would be acceptable, so that parts of the Readme that aren't supported by Hackage wouldn't be mangled in the resulting Haddock contents page output, e.g., at the bottom of this contents page.