Jefferson was an athiest too, and he wrote that text.

The Declaration of Independence is a statement of values, a list of the ways the Crown had violated those values, and a list of the ways they felt were proper to address those violations, up to and including armed revolt.

The Constitution was an attempt to make a goverment based on those values. It was and is flawed, and should be changed to better reflect those values. That's why "What about the 3/5 Compromise?" isn't a gotcha. It's wrong, everyone knows it's wrong, schoolchildren are taught it's wrong by the government itself.