Depending on who you‘re dealing with you don‘t have to fear punishment by the church at all. Cases like murder usually were dealt with by the secular justice system anyway. You would be on trial and they didn‘t need your confession to sentence you. Just evidence or believable, independent witnesses.

In the cases of Jeanne D‘Arc or the Templars the situation was heavily politicized and they were likely tortured to force a confession. This would be considered highly irregular of course but it still happened. Very similar to how governments torture people against their moral codes and laws today when people in power believe the goal justifies the means.

It was important for the English to strip Jeanne off her prophet status and many of them probably simply didn‘t believe her anyway. It sounds all a bit whacky after all. And Jeanne, being the devoted believer she is, knew god was her witness. She was willing to die an agonizing death just so she doesn‘t have to live a lie. Same goes for the Templars.

I guess no matter how you look at it, religion still killed these people. I won‘t debate that.