Ok, since you're advocating for Obama to break the law here I don't want to hear you complaining when you think he broke the law doing something else.
No. While I'm not going to go look up the exact language of the defense appropriation, I'm quite sure that it simply says 'no funds will be spent', not 'no DoD funds will be spent'. While federal spending is often broken up by topic, its rules are binding on all parts of the federal government. This is why you end up with random, unrelated amendments sometimes tacked on to bills.
I'm not sure what the total bill for housing and trying all these detainees over years would be but it's unlikely that any civil rights organization has the cash for that.