I am limiting the survey to the 20th century for an apples to apples comparison. Applying 21st century values to to 15th century tends to be anachronistic.
Worst theocracies:
Islamic Republic of Iran: extrajudicial killings, torture, repression of political opposition, secular intellectuals, and free press.
Kingdom of Saudi Arabia: Beheadings, political assassinations, repression of women, totalitarianism..
Taliban: beheadings, execution of homosexuals, adulterers, heretics. Intolerance for religious minorities, destruction of historic world heritage archeological sites.
State Atheism - worst atheist regimes:
Soviet Union: murder of hundreds of thousands of priests, deacons, Christian laypersons in the name of State atheism. Widespread oppression and arrests of Orthodox Christians, Muslims, Baptists.
Khmer Rouge: Murder of tens of thousands of Buddhist monks and laypersons.
Communist China: Destruction of Buddhist temples, Christian churches, widespread oppression of religious minorities.
Worst theocracies:
Islamic Republic of Iran: extrajudicial killings, torture, repression of political opposition, secular intellectuals, and free press.
Kingdom of Saudi Arabia: Beheadings, political assassinations, repression of women, totalitarianism..
Taliban: beheadings, execution of homosexuals, adulterers, heretics. Intolerance for religious minorities, destruction of historic world heritage archeological sites.
State Atheism - worst atheist regimes:
Soviet Union: murder of hundreds of thousands of priests, deacons, Christian laypersons in the name of State atheism. Widespread oppression and arrests of Orthodox Christians, Muslims, Baptists.
Khmer Rouge: Murder of tens of thousands of Buddhist monks and laypersons.
Communist China: Destruction of Buddhist temples, Christian churches, widespread oppression of religious minorities.