Hotdog - you're quite right. A simple bolt would be effective and cheap; however, my experience on freighters is that ground staff are on the upper deck much sooner than on pax flights and having to get out of the seat to unbolt the door would interrupt post-flight checks and duties. Far better to fit a coded system as per pax a/c, with a code known to the ground engineering staff and a simple opening handle from within.
Anti-terrorism measures are usually 'catch-up' ideas - in this worrying incident, we have the ability to pre-empt flight deck intruders with a simple measure. After all, a fully fuelled freighter would be just as devastating a weapon as a pax a/c. Ways of improving security at cargo operations are being looked at now, but it would appear that nothing is being done in a hurry. Perhaps the SIA Cargo incident and the FedEx (or UPS?) incident just a few years ago, where someone managed to be 'posted' to his destination on a cargo flight (he was spotted by the delivery driver at home address!) -may put more priority on cargo flight security.