Cringely on Domestic Eavesdropping
I'm not sure I'm following your argument. Are you saying that since Padilla was indicted on charges not related to terrorism that he couldn't have been guilty of that as well? I don't think that is a reasonable assumption. More likely, the justice dept. thought that it would be easier to obtain a conviction on the charges they presented or that they did not want to expose intelligence gathering methods in a civilian court.
I think you have to look at a redefinition of battlefield when dealing with terrorism. The battlefield is where they choose, and they generally choose civilian targets. Much of our thinking is outmoded when it comes to fighting a threat like terrorism. There is no surrender of the enemy to mark the end of hostilities. Victory consists largely of being able to avoid or limit attacks.