Personally I think UncleMeat's criticism is dead on and exactly why as you say Jon should take the historical argument out. Although you'd get a much less pithy title without collapsing civilizations.

Arguments about sourcing feel like face saving rather than legitimate criticism of the view bought forward by UncleMeat. After all the original video is completely unsourced but apparently beyond reproach in that regard. Also where we have sourcing (for example the Dark Ages wiki) it only strengthens the point made by UncleMeat as they were indeed correct about the views of historians.

More broadly if we want discussion to be well sourced we shouldn't apply that selectively and in particular selectively against the people who disagree with us.