I use org mode extensively, and had added Zack's workflow for integrating mutt with org mode to my ~/.emacs some time ago.

However, I've been annoyed that refiling closes the org-capture frame before refiling finishes. The following trivial modification to Zack's code (which I previously modified to work with org-mode >= 0.8) waits to close the frame until you've finished refiling.

(require 'org-protocol)
(add-hook 'org-capture-mode-hook 'delete-other-windows)
(setq my-org-protocol-flag nil)
(defadvice org-capture-finalize (after delete-frame-at-end activate)
  "Delete frame at remember finalization"
  (progn (if my-org-protocol-flag (delete-frame))
         (setq my-org-protocol-flag nil)))
(defadvice org-capture-refile (around delete-frame-after-refile activate)
  "Delete frame at remember refile"
  (if my-org-protocol-flag
        (setq my-org-protocol-flag nil)
(defadvice org-capture-kill (after delete-frame-at-end activate)
  "Delete frame at remember abort"
  (progn (if my-org-protocol-flag (delete-frame))
         (setq my-org-protocol-flag nil)))
(defadvice org-protocol-capture (before set-org-protocol-flag activate)
  (setq my-org-protocol-flag t))

Now, the frame automatically disappears after you refile it, keeping my refile.org clean.