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Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
Taken literally, there's nothing in there about the inalienable right to burn stuff.
By contrast, the right to "denounce" or criticize things -- which is what he was doing -- is in there.
If saying you don't think somebody should do something is violating their 1st Amendment rights, then there are no 1st Amendment rights.
From the WSJ:"Most Afghans learned about the Quran burning in Florida only when Mr. Karzai on March 24 (4 days after!) condemned the act as "a crime against the religion and the entire Muslim nation," called on the U.S. and the U.N. to bring the perpetrators to justice and demanded "a satisfactory response to the resentment and anger of over 1.5 billion Muslims around the world."
General Petraeus certainly won Karzai's heart and mind. /s