The main problem will be that the email protocols SMTP and IMAP simply don’t have any MFA integrated and defined, so no good news on that front. As mailcow basically only taking use of open-source software like dovecot and postfix to offer SMTP and IMAP capabilities, mailcow/MDM won’t help here I think.
Not sure how other companies, not using Exchange, are solving this. Maybe you know someone you can check with how they solved that?