I noticed the dilemma of the author's knowledge playing itself out, too--in some ways I actually thought Fever, 1793 solved the problem most elegantly, since Andersen has the Benjamin Rush vs. the French doctors (with Rush being basically a medieval quack, and the French being modern) debate play out within the book, and actually have readily observable consequences for the protagonist and her family. I live right near Philadelphia, actually, and it was something of a shock to see Rush taken down those pegs, since he's still something of a favorite local son.

In general, living near Philadelphia, I thought Andersen did a great job of capturing it as it was at the time--which isn't surprising, since she lives in the PA suburbs of Philly.