It's hard to understand because..
a) most people probably have little understanding of military awards outside of hollywood and might be forgiven for thinking they are all given for combat
b) most managers, whether in the military or not, seem woefully clueless about the impact of cumbersome poorly designed systems and the payback on well designed ones (or well designed hacks running on top of the poor system) So that someone even noticed he was more productive, didn't freak out because he did something different, didn't freak out because the different thing involved "programming" *AND* gave him a medal... seems pretty remarkable.