Rat Boy Walker is small fry. As long as he's kept in custody, he can't do much harm. And the antics of his lawyers serve to discredit the lawyers defending these scum, and make it now politically possible to try further operatives captured, whether citizens or not, especially dangerous ones whose trial in civilian courts could do a lot of damage, before military tribunals. This guy Padilla is the first example of that.
I wonder if the death penalty will be sought in his case. I wonder if he had any co-conspirators in this country. The fact that he tried to go to his home turf in Chicago suggests that he did.
Matter of degree and ability to prove direct military/paramilitary action specifically against the US, perhaps? Johnny was simply a foot soldier in Afghanistan. Jose was an in-our-country operative looking to nuke us.