Atheism is Indeed A Civil Rights Issue

This hasn't really happened since Roman times.

Not Exactly.

From Wikipedia:

The Soviet Union was the first state to have as an ideological objective the elimination of religion. Toward that end, the Communist regime confiscated church property, ridiculed religion, harassed believers, and propagated atheism in the schools. Actions toward particular religions, however, were determined by State interests, and most organized religions were never outlawed.

Some actions against Orthodox priests and believers along with execution included torture being sent to prison camps, labour camps or mental hospitals.[11][12][13][14] Many Orthodox (along with peoples of other faiths) were also subjected to psychological punishment or torture and mind control experimentation in order to force them give up their religious convictions (see Punitive psychiatry in the Soviet Union). [12][13][15][16]

It is estimated the some 20 million Christians (18 million Orthodox, 2 million Roman Catholic) died or were interned in gulags under the Soviet regime 2.7 million martyred under Stalin.[17]

Practicing Orthodox Christians were restricted from prominent careers and membership in communist organizations (the party, the Komsomol). Anti-religious pro da was openly sponsored and encouraged by the government, which the Church was not given an opportunity to publicly respond to. The government youth organization, the Komsomol, encouraged its members to vandalize Orthodox Churches and harass worshipers. Seminaries were closed down, and the church was restricted from using the press.

I can give specific examples if needed.