Umm, Weren't They Already Desecrated?

The U.S. and NATO and doing all sorts of gymnastics trying to apologize about some NATO soldiers trying to burn some Korans and then some out of control Muslims protesting like Occupy Oakland thugs.
From Fox News: From the BBC: The Nato commander in Afghanistan has apologised over reports foreign troops may have burnt copies of the Koran.
Announcing an inquiry, US Gen John R Allen said any "improper disposal" of religious materials was inadvertent.
Reports suggest the books were taken from prisoners after the US uncovered a secret Taliban message system.
Rumours that a Koran had been burnt led to protests outside the US base at Bagram north of Kabul. One man was hurt when Nato troops fired rubber bullets.
President Hamid Karzai condemned the reports that the Koran had been burnt, as did the Taliban who said the incident would hurt the feelings "of one billion Muslims around the world".
US Defence Secretary Leon Panetta called the incident "inappropriate and deeply unfortunate".
"These actions do not represent the views of the United States military," Mr Panetta said in a statement apologising to the Afghan people. He promised to review the results of the investigation.
http://www.bbc.co.uk/news/world-asia-17110079
So, if the Korans already had secret Taliban messages written in them, weren't the Korans already desecrated? 
I realize that the Army has to reduce tensions, so they will probably throw some soldiers under the bus because they soldiers acted correctly when they burned the Korans.  Maybe they could have handled it better, but the bottom line is that the Korans needed to be destroyed or they could have ended up in the hands of the enemy in which we are at war with.  And if a Christian did this to a bible, I would have no problem with the military destroying the bible rather than having a chance they may get into enemy hands.
If the Muslims don't want the Koran  burned, then maybe they ought not to be writing secret messages in them.