Cross examination starts on page 22 ...
I'm sure she envisioned what was at first a symbiotic colonial relationship rather like lichens or stromatolites gradually becoming increasingly intertwined.
I can guess how Behe would lawyer his point. There's no halfway position in the difference between any particular given bacterial body being inside any particular given archaebacterial body and being outside of same. Well, there is, but it's the halfway point of a grape disappearing into your mouth.
Nevertheless, that doesn't mean suddenly one day all over the world all the bacteria that had been outside of an archaebacterium the day before were now inside of one. There could have been a very slow transition from all-external to all-internal symbiosis and I'm sure that's what most scientists mean now when they say they accept endosymbiosis theory.
I think someone (Margulis herself, perhaps?) could call Behe on that.