Hmm... I've heard Behe speak, and he insists that he accepts common descent of organisms as a fact. He's written that in several places.
Do you have anything he's written or stated to the contrary?
At the 1995 meeting of the American Scientific Affiliation, Kenneth Miller debated Darwinian theory with Behe. Miller argued that the 100% match of DNA sequences in the pseudogene region of beta-globin was proof that humans and gorillas shared a recent common ancestor.
Behe said he agreed that it was true, and said that he had no problems with common descent of organsisms.
If I was a creationist, I would be very wary of Behe; he could easily convince many creationists to become theistic evolutionists as he is.