It's looking like Newsweek was right...
Not exactly.
Newsweek's report was based, not on an FBI report, but on the accusations of a well-known ex-detainee after his release--an accusations shown to be without merit, as that same detainee had never mentioned such an incident before in any of the many interviews they gave, and in fact said that his treatment was good.
Even if it turns out that some other guard had disrespected some other detainee in this way, it would not make Newsweek's original story "right". If I accuse you of child molesting for no reason and then it turns out that you robbed a bank, I am not "right" just because in both cases you did a criminal action.
As an aside, this "revelation" seems awfully suspicious: Newsweek carried a story about prisoner X saying the Koran was flashed down the toilet? It was wrong? Quick, everybody--find us a story about anybody in Guatanamo bay who claims the Koran was mistrtreated in any way that has to do with toilets!