At this point I've used up all my arguments, so I'll leave you with another great piece from the same guy. http://www.strangenotions.com/why-history-isnt-scientific/
Most people in the modern atheism get there by way of science, and they looooove science, and I mean physically. But history, especially ancient history, is a very different field and research is conducted very differently and certainty is much harder to establish. So a line of evidence or lack of it can be very convincing to the scientifically inclined but not really mean much to a historian.
I read that, and I've got to say it sounds like the author has a dog in this fight. His notions of "certainty" and "proof" in the sciences are flawed; at least on the pedantic level he's approaching the layman's knowledge of history with. If he doesn't get his science strawman right, why should I trust him on history?
Plenty of sciences deal largely with looking into the past. Forensics, astronomy, and paleontology come to mind; paleontologists arguably deal with a far more piecemeal, rearranged, and destroyed record of events than written history. The scientific method helps even when you aren't literally repeating past events in the lab.