The problem you're encountering can't be exactly as you describe, because our EFI implementation doesn't yet include Secure Boot functionality at all... there is nothing to disable. The absence of Secure Boot support in our firmware shouldn't prevent you from booting a Secure Boot enabled OS though, unless the guest OS itself (or its bootloader) is explicitly designed or configured to fail in the absence of Secure Boot.
Might be worth checking the grub.cfg or menu.lst (or whichever config file ends up being used) to make sure that it is still sane. That would seem to me to be the most likely point of failure.
Cheers,
--
Darius