If you're going to go and say "religious freedom did not exist back then" it leads onto the question, "does true religious freedom exist today, or is it just varying degrees of tolerance?". Perhaps the title is a poor one, but whilst we must keep away from simply imposing modern conceptions on medieval ones, it is vital to recognise that neither now nor then were these things truly set in stone.
... and whether you view humans as intrinsically moral creatures or creatures who use morality because it is beneficial to do so, the result is often the same (we're all bound tightly by social norms after all).