The fact that bin Laden is not wanted by the FBI for the 9/11 attacks has generated a small stir online (but not in the "real" media). A typical example: http://onlinejournal.com/artman/publish/article_912.shtml
It seems that the decision to seek a (supposed) al Qaeda small fry's conviction and death was meant to appease the public (though it hasn't).
Meanwhile, al Qaeda bigs are being held overseas as "enemy combatants" and might face a military tribunal -- some day. Notice that by putting off court adjudication indefinitely, the government can carry out aggressive actions -- including the various national security gimmicks used to KO the Bill of Rights during wartime -- without having to prove anything about the alleged conspiracy.
However, don't you think that if there were strong evidence against bin Laden that the government would have rushed head-over-heels to obtain an indictment?
The desire to avoid indictments stems from the desire to short-circuit the freedoms that define America as a free country while not drawing attention to holes in the White House conspiracy theory.