Isn't the problem Guantanamo itself?

In the middle of this furor over the recent Newsweek article and retraction, I have to ask: Is the problem one badly-sourced paragraph in a news report, or the fact that we're running a detention facility under almost bizarre secrecy at which we're loudly proclaiming that we're not obliged to honor the Geneva Conventions?

We've been hearing reports of questionable practices at Guantanamo Bay for more than two years now. The place is an abomination--not a POW camp, nor a jail, but something undefined with all the rules of Calvinball.

I know folks on the right object to treating the "war on terror" as though it were a criminal matter, but could we at least consistently treat it as though it were a war? This "9/11 justifies damn near anything" mindset is dangerous--as we're now seeing.