"When have people ever been tortured or killed in the name of atheism?"

Stalinist Russia. Not all of the people killed under Lenin and Stalin were killed because of their religion, but many were. Churches were looted and burned, nuns were raped and killed, priests and bishops and monks and laypeople were killed because they were Christians by people whose motivation for doing so was their atheism.

They were killed in the name of communism, as were the victims of Mao. Religion was not seen as a threat to atheism, but to communism. Not the same thing at all. Correlation is not causation.