I've also been trying to deal with this issue recently. I'm wary of disabling auto-saving, so I've done two things:
(1) Keep mbsync from syncing them:
--8<---------------cut here---------------start------------->8---
;; based on:
https://emacs.stackexchange.com/a/24430
(defun draft-auto-save-buffer-name-handler (operation &rest args)
"for `make-auto-save-file-name' set '.' in front of the file name; do nothing for other operations"
(if
(and buffer-file-name (eq operation 'make-auto-save-file-name))
(concat (file-name-directory buffer-file-name)
"."
(file-name-nondirectory buffer-file-name))
(let ((inhibit-file-name-handlers
(cons 'draft-auto-save-buffer-name-handler
(and (eq inhibit-file-name-operation operation)
inhibit-file-name-handlers)))
(inhibit-file-name-operation operation))
(apply operation args))))
(setq bms/mu4e-mailbox-list '("myunimail-maildir" "myothermail-maildir" "yetanothermail-maildir" "whatsthis-maildir" "etcetc-maildir"))
(setq bms-draft-dotting nil)
(defun bms/draft-dot ()
(when (null bms-draft-dotting)
(dolist (mbox bms/mu4e-mailbox-list)
(let ((draft (concat mbox "/Drafts/cur/")))
(add-to-list 'file-name-handler-alist `(,draft . draft-auto-save-buffer-name-handler))))
(setq bms-draft-dotting t)))
(add-hook 'mu4e-compose-mode-hook #'bms/draft-dot)
--8<---------------cut here---------------end--------------->8---
(=draft-auto-save-buffer-name-handler= seems to get clobbered by something else during init, so I just delay setting this until the first time I compose a mail to get round this.)
This prevents remote mailboxes from getting cluttered.
(2) When I know I don't have any drafts I need, run:
--8<---------------cut here---------------start------------->8---
(defun bms/delete-all-mu4e-drafts ()
(interactive)
(shell-command "mu find flag:draft --fields \"l\" | xargs rm"))
--8<---------------cut here---------------end--------------->8---
to clean things up.
--
'(Benjamin Slade ("he/him") (
https://lambda-y.net )
`(pgp_fp: ,(21BA 2AE1 28F6 DF36 110A 0E9C A320 BBE8 2B52 EE19))
"sent by mu4e 1.6.6 in GNU Emacs 28.0.50 on Arch Linux")