gistfile1.el

;; ~/*.org に対して ORGMODE-Markdown を適用していく
(let ((exporter (assoc "Markdown" org-generic-alist))
      bufname)
  (if nil (error "ORGMODE-Markdown is not loaded.")
    (flet ((read-char-exclusive () (plist-get (cdr exporter) :key-binding)))
      (dolist (orgfile (directory-files "~" t "\\.org$"))
        (setq bufname (find-file-noselect orgfile))
        (with-current-buffer bufname
          (org-export-generic nil))
        (kill-buffer bufname)))))

flet + read-char-exclusive で解決した！