What about people executed for heresy in the Papal States? There are many examples, but the most famous would be Giordano Bruno, burnt at the stake for heresy in Rome in 1600.

The whole "it was the civil authorities not the Church" line doesn't really work there, since the Pope was ultimately in charge of both, even if the two were still nominally distinct.

Even in the case of the Spainish Inquisition, where the Church-va-State distinction was somewhat more real – you have to ask whether the Church encouraged or discouraged the civil authorities from imposing capital punishment on those it convicted of heresy. I think you will find that the answer was very much "encourage", not "discourage" or neutral. "We didn't execute anybody, we just encouraged the government to execute them" is a rather laughable defence.