He got the numbers by adding up the numbers listed in the newspapers, including Taliban press releases, multiple reports of the same event, and so on. The 3800 dead figure is just plain wrong.
The Associated Press reports that the number of casualties was between 500 and 600, which are one-eighth to one-sixth of Herold's numbers. Even Human Rights Watch thinks that the actual number of casualties was probably between 1000 and 1300, about a quarter or a third of the Herold's number. Given that HRW in turn has an institutional bias to inflate the numbers, I'd say their numbers represent a solid upper bound on the number of civilian casualties in the Afghan War.
I'm dubious that the casualty totals have much to do with whether or not one supports or opposes the Afghan War, but we might as well use the correct numbers while descending into flames. :)