Question: At the end of the episode, the military shows up and asks for all the evidence as it was a matter of national security. It's quite obvious that Harry called the military and was stalling for time until they could show up and get the evidence. Why did Harry call the military? I seriously doubt that it had anything to do with national security. I believe it was because he was actually trying to let Irene off the hook.
Answer: He wasn't necessarily trying to let Irene off the hook. He still found her guilty. He was trying to get the diary out of evidence, but he had no legal standing to do so. It had nothing to do with military officials listed, but the fact that at least one of them talked about the military's equipment (the bombers). Harry called the military in hopes they could remove the diary from evidence. The major briefly reviewed the diary and classified it temporarily as "Secret", meaning that the court could no longer introduce the diary as evidence, which would have made the contents public (since there's no confidentiality laws between prostitutes and their clients).
Answer: It's possible when Harry called the military, he implied that the book contained sensitive information, seeing as how many government and military officials were part of the client list.
I thought it was because he developed feelings for the madam and couldn't bring himself to turn her in.