Seems a bit broken to claim that something that happened in 1689 when it was a colony, as you explicitly note, is fundamental to the founding of the nation a century later.
“The deepest bias in the history of the American people,” according to Arthur Schlesinger. “The most luxuriant, tenacious tradition of paranoiac agitation in American history,” said John Higham.
https://www.theguardian.com/world/2015/sep/12/america-histor...
I say this as an American Catholic who went to Catholic schools until college and knows full well about Catholic discrimination in US history. Protestants have discriminated against other protestants, everyone has discriminated against LDS, LDS has discriminated against everyone else, everyone has discriminated against Jews, Catholics have discriminated against <insert your choice of target here>, etc. These facts don't make up founding motives just because they are true.