Well, you don't "have" to question it with science. From a religious vantage point it's certainly valid to question evolution (or anything else) with religion. And it can be questioned with philosophy, or from an ethical standpoint, etc.
How far you might get in that approach is another matter, as is whether you're going to make any headway with someone who doesn't share your premises.
The real problem, however -- and I think this is the point you're actually making -- is that Behe et al are *pretending* that they're using science to challenge evolution, when they're actually basing their objections on something else. They're dishonestly trying to give their religious misgivings about evolution the procedural authority of real science, in order to deceive the public about the validity of their "rebuttal". They're falsely claiming that their religious/philosophical dissatisfaction with evolutionary biology has met the high standards of scientific discovery and validation, when it most certainly has not.
Yes, that is exactly what I meant. If one's objection to the science of evolution is to be given the imprimatur of science, that objection must itself be scientific. And Behe et al.'s objections, as you correctly noted, are not scientific.