The stakes can indeed be high. However risk exposure (impact multiplied by probability) is often less than people think. An operational order betraying a strategy, for example "take Wimbledon Common at 4am tomorrow," must remain secret only until the order is carried out. So (gross simplification) any encryption that takes longer than from now to 4am tomorrow to break will suffice.

The harder problem is guaranteed delivery, which is impossible using only technology. You might email that order to the General in charge, and if he's out on a toke and doesn't read it within 5 minutes forward the order to his 2IC. And if the 2IC is on the john your only recourse is to forward the message to the nearest permanently staffed guaranteed action point (GAP). The GAP will send out one or more despatch riders to hunt the recipients down in meat space and deliver the message.

In any other scenario the same security best practices apply as in the commercial world, albeit with much more money.

Edited for spelling.