Irrelevant.
What IS relevant, is that a system of enforced atheism proved to be every bit as (if not more) brutal, corrupt and irrational as any other system, including those which are considered theocratic.
The demand that all individuals adhere to a strictly-humanistic belief system (itself another form of religion), brutally-enforced by the state, stands counter to the ideals of individual choice and true enlightenment.

However, the perpetrators of these injustices believed (as you would appear to also believe) that they were enlightened thinkers, casting off the shackles of "superstition" (it should be noted, more often than not, people who accuse religious believers of superstition, fundamentally misunderstand those faiths, many of which stand diametrically-opposed to superstitious practices).