I got back to this task at hand, and this elisp command works just fine (based on export testing of a bunch of Org files).
Let me know if I missed out on something (or did over-lower-casing) :)
(defun modi/lower-case-org-keywords ()
"Lower case Org keywords and block identifiers.
Example: \"#+TITLE\" -> \"#+title\"
\"#+BEGIN_EXAMPLE\" -> \"#+begin_example\"
Inspiration:
https://code.orgmode.org/bzg/org-mode/commit/13424336a6f30c50952d291e7a82906c1210daf0."
(interactive)
(save-excursion
(goto-char (point-min))
(let ((case-fold-search nil)
(count 0))
;; Match examples: "#+FOO bar", "#+FOO:", "=#+FOO=", "~#+FOO~",
;; ",#+FOO bar", "#+FOO_bar<eol>", "#+FOO<eol>".
(while (re-search-forward "\\(?1:#\\+[A-Z_]+\\(?:_[[:alpha:]]+\\)*\\)\\(?:[ :=~]\\|$\\)" nil :noerror)
(setq count (1+ count))
(replace-match (downcase (match-string-no-properties 1)) :fixedcase nil nil 1))
(message "Lower-cased %d matches" count))))