Currently it is possible to configure both PGP and MIME for one identity. However, I did not find a method to choose per mail, which one of the two to will be taken. As there are already buttons for signature and encryption, maybe you can extend them like the attachment/answer/... button to provide the key selection, when doing a long press.
Sorry, meant OpenPGP/MIME vs. S/MIME.
You can find select the Cryptographic Message Format via the Menu (Options->"Cryptographic Message Format") there you find all four possibilities.