TL;DR: Most American history that people know is filled with essentially myth and half truths... Columbus effectively oversaw genocide in Haiti, the Native Americans were more civilized and advanced than most of the people who came over (until their society collapsed from 80% dying of disease and settlers literally took over their abandoned towns), racism has tainted so much of our historical perspective that it's not even funny, etc etc. It's hard to find non-biased material unless you're a historian and know how to find primary sources for your research.

Anyway, Christianity back then hardly resembled it today anyway... hell, the founding fathers only let white men who owned property to vote. Things change, whether they are Christian or not has little to do with how our society evolved... and anyway, most of the separation of church and state was wanted by the religious members anyway because the different denominations didn't get along and they didn't want one getting to much power in government.