My point of view is this:
Lindh is a scapegoat plain and simple, the classic "in the wrong place at the wrong time". I highly doubt that even if he was Al Qaeda that he was anything other than an ordinary grunt. Rightly or wrongly, he was charged and will now sit out 20 years in prison to satisfy, in part, the U.S. need to show that terrorists/militants cannot get away with their actions. This guy was young and dumb, and bought into an ideology which, having not gotten him killed, will result in him sitting in a jail cell.
As former military, I don't care what you call your enemy, but no soldier should ever be charged with any type of offence short of crimes against humanity. I'm not sure which U.S. laws Lindh violated, but even if he did break them, he did so offshore i.e., he was not a spy, did not commit his crimes in the U.S., etc. As far as I know, he did not personally kill any U.S. citizens (other than, perhaps, by returning fire on U.S. troops IN AFGHANISTAN during a declared war). So, at the end of the day, he goes to jail.
It is classic U.S. policy to say, on the one hand, that U.S. jurisdiction extends across the planet, but, on the other hand, that U.S. troops should be excluded from the jurisdiction of the International War Crimes Court. If you want to thrown a young, dumb John Walker Lindh in jail...so be it....but everybody should be playing by the same rules, and if that means that some poor AC-130 pilot is dragged before the court for taking out a wedding (not to suggest it was intentional, just a friendly fire mistake), then so be it as well. Let both of them be judged
Which brings me to my next point. Can someone explain to me why Lindh, a U.S. citizen, was entitled to a trial and counsel, but the other high profile Taliban/Al Qaeda U.S. citizen (think "Hamdi" is his name) is not? Again...one set of rules for everyone, no one is above the law, and if the U.S. has any hope of ever promoting freedom and democracy around the world (wasn't that what Dubya said this was all about anyway), better that it do so by setting good examples rather than labelling people "enemy combatants" out of convenience and throwing them in jail cells in sunny Guantanamo, denying to the "enemy" the very values and principles that they cherish so much.