The difference between an act of war and a criminal act is this:
An act of war implicates many. We take the entire Taliban as our enemy.
A criminal act implicates few. We take those suspected of specific crimes as peers whose guilt we are to judge later.
Why we should afford domestic criminals more rights than we afford Osama bin Laden:
Domestic criminals have the rights guaranteed to them by the US Constitution as a privilege of birth, an inheritance. It's not fair that they have more rights than the Chinese or the Afghans, just like it's not fair that the children of rich kids get more presents at Christmas than the children of poor kids.
Whether we make ourselves like the terrorists by acting unilaterally, instead of through the UN or the World Court:
The crime of the terrorists is not the disapproval of the World Court. The crime of the terrorists is that they targeted civilians. Acting in our own defense does not make us like the terrorists because we do not target civilians. We might cause civilians to die as we pursue our military objectives,but we don't target them.
One can compare al-Qaeda and the US at any level of abstraction that one wishes. On the most particular level (who gets attacked, how, and why), al-Qaeda and the US are different. On the most abstract level (groups pursuing their geopolitical goals through some means or another), al-Qaeda and the US are the same. No individual level of abstraction is the "right" or "true" one. To the question "Are al-Qaeda and the US morally equivalent," the answer is "Yes or no, depending on what level of abstraction you choose to employ." Those who wish to see moral equivalence choose a high level of abstraction. Those who wish to see moral difference choose a lower level of abstraction. The dividing point is probably the issue of targeting civilians. At a certain level of detail, the difference between targeting civilians and not doing so differentiates the US from al-Qaeda. At a certain greater level of abstraction, this difference disappears.
Whether holding our intelligence services to a higher standard leads to better security in the long run:
That's theoretically possible.
It's also possible that it's impractical to expect us to be able to gather evidence against foreign enemies as readily as we do against domestic criminals, and that holding ourselves to this high standard just mean that terrorists generally get away, and that we wind up more vulnerable.
Whether the terrorist threat is primarily to our safety or to our integrity:
If you can downplay the military threat to our nation by saying that terrorist attacks can't destroy the US (only injure it), then I can downplay the political threat to our freedoms by saying that John Ashcroft can't destroy them (only injure them).