Anything you move over to the airgap computer should be through usb stick and then the usb stick essentially smelted.
It would be safer to use QR codes rather than USB devices (due to potential attack vectors) but if you are going to use USB there is no reason to "destroy" the device (the point is to simply not re-use it).
I guess I like to say destroy because then I cant use it on network (or someone else) ever again on purpose or by mistake compromising my whole network. Even if I marked the devices in red it could still happen if a family member, TSA, boogyman etc gets there hands on it and says "what's this" and plugs it into a computer (which 2014 will be 99% likely on network) now your whole op is compromised because of someone intentional or otherwise.
Additionally I am not quite sure I understand how QR codes keep you safe from malware. Please correct me if I am wrong but computers communicate using the most basic of 1's and 0's. In theory if the QR code program on each end was malware. It could simply decode the QR data and format it to do whatever corrupt bidding you could fit on a QR code (no idea). I do know that when I was a kid I programmed a basic hard drive delete program. It was so small if I had to guess I could get it into QR format somehow.... could be way off base tho but makes sense in my head at least.
**edit** I guess you're saying that because my airgap computer is snapping photos of the QR codes and the airgap comp never touches the network that there is no way for the airgap comp to transmit back data w/o it generating its own QR code. wireless signal, Lan, IR, etc etc. If that makes sense. Even if they were to encode my private keys into a QR code it could never make it back to the network because the airgap computer physically has no way of talking.