No.
The jury need only accept that he was there to help those who he knew were to kill, and had killed, Americans.
Obviously he was so, yes, the case is pretty much over.
I think they may have to prove that he "helped" after he knew. Also, the word "kill" can also be used to describe the actions of soldiers in combat. I would think that the prosecution needs to prove that Lindh helped those who he knew were to murder, or had murdered, Americans.
Also, unless the claim is made that just being there constitutes help, then Lindh may have to have been found to have committed some overt act which assisted the conspiracy. Lindh's most noticeable act was to surrender. It is not clear to me how that would aid the Taliban or the Al Qaeda.
Conspiracy law does not actually require that every conspirator engage in an overt act in furtherance of the conspiracy. However, the prosecution does have the burden to prove that Lindh was a conspirator; that is, that he agreed to the commission of some illegal act.
One of the key problems, I believe, with the RICO act is that it relieves the prosecution of some of the burden of tying conspirators to the same illegal act or related acts. I don't know how far the idea can be stretched to find Lindh guilty of conspiracy to murder the people in New York just because he hated them and moved to a country where many other people hated them.
As for the death of the CIA man, I don't know whether it is reasonable to hold every Al Qaeda and Taliban member individually guilty for every death which occurred in Afghanistan. As a prisoner, Lindh was not free to leave the prison and thus his presence their does not constitute very convincing evidence that he willingly agreed or had knowledge of everything planned or done by the other prisoners.
Many would suggest that Taliban who became aware that the US had decided that they were an enemy, had an obligation to throw down their arms or risk being held accountable for the crimes of the Al Qaeda. But then, that is exactly what Lindh did. He threw down his arms and surrendered.