I agree with you, but we're off on another tangent. If the question is: Should soldiers be tried in civilian courts, then my answer would have to be: No. You'll get no arguments with me on this whatsoever. However that's not really the question here. President Bush isn't even arguing that he'd veto the bill based on the treatment of soldiers. He wants the CIA exempt, not the infantryman.
Which means I'm not entirely in agreement with Bush, who is trying to thread the needle as he often does.
How can you try a CIA man for actions taken at a secret facility in a secret third country without access to classified intelligence? It can't be done. To attempt it is to subject intel agents, in war, to a civilian court, and to force classified information into the open.
The governments who have offered our agents a safe zone would be exposed, secret agreements allowing our people to operate there would be exposed. Lawyers who would never risk themselves in wartime would be assigning themselves the right to pass judgement on the ones who do. Obviously my concern here is for the infantrymen as surely as the CIA agent.
The response to this would be to drive intel activities further into the shadows, which I believe should happen anyway. When you make spying a career path with a regular salary and a retirement package you've already hamstrung yourself when by its very nature it is supposed to be felonious behavior.