The normal procedures of American justice were finally allowed to work. There was never a reason to subject Citizen Padilla to anything less, all the prior excuses notwithstanding.
Of note, the more serious accusations against Padilla didn't make their way into the charges, including the claims of a plot to set off a "dirty bomb" in the US:
The charges brought in civilian court in Miami, however, were a pale shadow of those initial claims in part because Padilla was interrogated about the plot when he was held as an enemy combatant for 3 1/2 years in military custody with no lawyer present and was not read his Miranda rights.
Get it? Torture and improper detention make it harder for the government to bring charges against the accused in court. (Although the "dirty bomb" plot turned out to be false.)
In short, the Padilla case was an example of what not to do in fighting terrorism. Dahlia Lithwick:
Of all the terrifically bad ideas implemented by the Bush administration since 9/11, probably the worst have involved torture. The decision to sideline criminal prosecutions and instead focus on "alternative interrogation" methods was wrongheaded from the get-go. It was wrongheaded as a tactical matter, wrongheaded as a legal matter, wrongheaded as an ethical matter, and wrongheaded as a matter of undermining world opinion. In fact the only thing the Bush administration has actually gotten right about torture is this one tiny truth: If you want to destroy someone-if that is your sole objective-torture works.