The period we're discussing was a VERY intolerant age --
with wars of religion, inquisitions, sundry persecutions.
It wasn't until after the Thirty Years War (1618-48)
that tolerance gradually began to pervade European thought.
Of course, if one arbitrarily selects certain biblical
passages and interprets them according to one's own
presuppositions anything can be justified. This is often
a perversion of the teachings of Christ and tells more
about the interpreter than is does about the Gospel. The
theologians and philosophers call this "absolutizing
the relative". I know of no instance in which Jesus
advocated violence or execution against those with whom
one disagrees. Much more could be said about the psychology
involved in religious intolerance but that would take a few
volumes!
Excusing sin because of extrinsic circumstances is called.... Moral Relativism.
Was Calvin a Moral Relativist?