Why is the government allowed to reverse engineer AND create laws making it difficult for citizens to do so?
Obviously the answer is that it is legal to reverse engineer something if you own it.
That said... I think there's an opportunity here:
EFF and other pro-reverse engineering organizations should sue and demand that the DOD follow the same laws that citizens follow.
If they lose the lawsuit, it be great ammunition (so to speak) for stopping anti-reverse engineering laws.
If they win... bonus!