Turns out to be quite simple:
(defun mark-spam (msg ignore)
"Mark messages flagged as spam."
(with-current-buffer (find-file-noselect (mu4e-message-field msg :path))
(goto-char (point-min))
(if (re-search-forward "^X-Spam-Flag: \\(.*\\)" nil t 1)
(string= (downcase (match-string 1)) "yes")
nil)))
(add-to-list 'mu4e-headers-custom-markers
'("Spam" mark-spam))
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