This a debate the country simply has never had. My personal feeling is that laws should not be (for lack of a better phrase) jury-rigged. If the material witness detention statute isn't quite the right tool with which to investigate possible terrorists, then it shouldn't be used to do so -- it's Congress' job to create those tools, and not the job of law enforcement to try and jam a square peg in a round hole. Ignoring little niceties like Constitutionality is a mistake, as anyone trying desperately to construct a case against Gitmo prisoners can attest.
[Judge] Smith rests his analysis in a critical assumption: That if the government is fighting terrorism by using the material witness statute pretextually to detain terrorist suspects, that detention is a criminal law detention rather than a national security detention. Judge Smith then looks at how the Fourth Amendment applies to criminal law detentions, and he sees the traditional criminal law arrest doctrine that requires probable cause that the person committed a crime. He then assumes that this is the only way to define probable cause, and when he sees that the material witness warrant doesn't measure up, he concludes that it must be unconstitutional.
I don't think that works. The point of pretextual use of the material witness warrant is to use them for national security purposes: the avowed goal is to try to investigate, monitor, and detain terrorists. Indeed, the pretext is that it's being used for a criminal investigation at all. And that's the allegation that al-Kidd makes in his complaint: it alleges that he was detained as part of a general program “to arrest and detain terrorism suspects about whom they did not have sufficient evidence to arrest on criminal charges but wished to hold preventatively or to investigate further." Given that, I think you have to define the "programmatic purpose" of the pretext as a national security purpose, and then confront the novel question (novel in the sense that no court has ever addressed it, as far as I know) of what kind of probable cause is needed under a United States District Court analysis for a national security detention warrant.
That said, I also don't feel that Ashcroft should be liable for prosecution on a 4th Amendment violation here. While it's not the job of law enforcement officials to construct adequate tools, the impulse to use the tools at hand to try and get the job done is an understandable and defensible one.
Which is not to say people shouldn't be held accountable for any mistreatment of al-Kidd while he was in custody, or that I agree with his detention in the first place. Just that I don't think he should be able to sue Ashcroft personally over it.