While I agree that this feature would be nice, it is unlikely to be done due to the way Enigmail interacts with Thunderbird. The division of duties between the two is pretty simple: we let Thunderbird take care of everything involving how the mail is accessed, and Enigmail takes care of how encrypted emails are presented.
What people are asking for here is "blow away the old copy of my email on the IMAP server and replace it with a new email containing the decrypted information of the old email." This involves a lot of email access issues: access, deleting, uploading, etc. This is stuff Thunderbird does, and stuff Enigmail very explicitly does not do.
POP access is little different. "Blow away the old copy of my email in the mbox file and replace it with a new email containing the decrypted information of the old email." The same issues arise.
While I agree that it would be nice if Enigmail did this, supporting this would likely introduce vast amounts of complexity to the Enigmail code. However, if Thunderbird could export an API we could use which would allow us to easily manipulate mail data, then we could support it pretty easily.
I guess the ultimate answer is "if you want this feature, you need to ask Thunderbird, not us." Sorry.