Six million Christians and Catholics in the 30-years war is going to be hard to beat for numbers in a relative short  period of time.    

The Holocaust had nine million but a lot of those were political prisoners, gypsies, mental defectives, Communists, labor unionists and such.  

The Jews matched six million number in the Holocaust, but the Jehovah's Witnesses were just  a tiny portion who actually were killed for their religion.  And the Jews were an economic issue as well as a religious issue.

Crusaders Death toll: According to Wikipedia’s list of wars and disaster’s death toll) is estimated to take lives of 1,000,000 (lowest estimation) up to 9,000,000 (highest estimation) between 1095 – 1291 religious wars.  But that's over a two hundred year period.