This feature has been requested periodically by many people, primarily because email searches cannot be performed on encrypted emails.
However, decrypting messages permanently is potentially a bad security practice. Once a message is stored unencrypted, it is vulnerable to compromise by anyone that has access to the computer or by any malware that could steal it and forward it to anybody. If a message was confidential enough to be encrypted, it should stay encrypted.
The matter is even worse when the email message is not stored on the local machine but on a POP/IMAP server instead. Not only this could potentially disclose the message to the whole world, but makes more difficult to implement the feature. Permanently decrypting the email message would translate to delete the encrypted message on the server and upload a new message containing the decrypted information from the original mail. This involves a lot of email access issues -- and email access is the email client's duty, not Enigmail's. Hence, implementing this feature would greatly increase the complexity in Enigmail, unless Mozilla provides someday an API to manipulate email data.
In short, permanent decryption is not supported in Enigmail, and is not going to be in the near future.
However, you can save the decrypted message as a text file via OpenPGP -> Save Decrypted Message.