I don't think there's an easy way out for this one.  You might do something like:

    (add-hook 'typo-mode-hook
              (lambda ()
                (when (and typo-mode (derived-mode-p 'markdown-mode))
                  (let ((map (make-sparse-keymap)))
                    (set-keymap-parent map typo-mode-map)
                    (define-key map (kbd "`") 'self-insert-command)
                    (push `(typo-mode . ,map)
                          minor-mode-overriding-map-alist)))))