Bradley Manning wants to become a female

That's how law generally works here, if you're guilty with no means of a loophole, you have to push the responsibility of the crime onto something or someone else. Their argument is essentially that if they were aware of his "crisis" and allowed him to keep said position, then that's the risk they took. So now it's his superiors fault for ignoring the red flags and not taking the necessary action

Well, it's like being secretly gay in a culture that prosecutes homosexuals. If society doesn't support & approve of your identity, it's a security risk because it makes you more vulnerable. IMO the right answer is "treat all humans equally," rather than not letting a given group join the army, but with the ridiculously insensitive treatment the army gives and has given to transgender individuals it's a pretty solid argument that it affected her mental state.