Damn you and your internal quote response.
Internal affairs is
outside of the police force?
That'd be like saying the Justice Dept, led by Eric Holder, is outside the executive branch.
To address the Judicial role, specifically as I see it being involved in this case-- I would say if the law enacted by Congress, ( the kill terrorist law, whatever) granted some unfettered power to the CIC,-- then the law is absolutely reviewable for being unconstitutionally vague; that's the tort, that the law failed, not how the executive branch failed to consult the Judicial Branch.
The idea that the Judicial branch should assist in, or dictate how a law is carried into execution is blatantly in violation of the separation of powers.