I have a similar situation in my work history. In my particular case I was consulting for a commercial firm with a duty of very strict confidentiality. Disclosing what I did for them would reveal their future consumer product plans. We discussed that I could freely disclose what I did as long as I didn't disclose who they were. So my resume has a line item marked "Client Confidential" and then I provide the technical details of what I did for them.

That's a bit harder to do in the case of classified material, but maybe there is a similar balance you can strike?