You're trying to justify it in the sense that they're some sort of smart people with a plan. They're just civilians, they're not spies. No malice or cunning elements to it - just idiocy.

The takeaway I got is that they just don't want people to visit Israel and made it as difficult as possible for me (which involved taking away my personal documentation, such as my invitation letter and copies of my citizenship, to give me a tough time when I got to Ben Gurion).