Is there any way to change this by using a plugin, modifying a config file, etc? Or is there any way to use Enigmail for S/MIME mails?
At the time of writing, this is not possible in Thunderbird. A ticket for this is opened in 2003 and has not been resolved as of yet. However, patches with options for SHA-2 signing and AES encryption have been posted already. Please refer to bug #222179 for more information.