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The only group which could legitimately lay claim to having been "exterminated by the tens of thousands" would be the Albigensians (a/k/a Cathars). While the crusade against the Albigensians was certainly regrettable and is a sad stain on the history of Christianity, let's keep a few things in mind:

The Albigensians were not Baptists, and were not Christians in any recognizable form. They had a strident hostility toward Christian marriage and childbearing (a result of their Manichaean beliefs) such that a person brought before the Inquisition on a charge of Catharism could win release simply by proving he was married.
The Church tried for 60 years to peacefully convert the Albigensians back to Catholicism. The military campaign was a last resort.
Had Albigensianism spread across Europe, their pacifism and the depopulation resulting from their rejection of marriage and childbearing, together with the massive depopulation of Europe resulting from the Black Death in the subsequent century, would have guaranteed the triumph of Islam throughout Europe. There would today be no Baptists, no Catholics, no churches, and no Bible.

The Albigensians were not Baptists, and were not Christians in any recognizable form

And what primary, confessional testimony supports that claim? I am not that interested in hostile testimony, not without the power of cross-examination, and not without the defendant being given the chance to speak for himself. I wish to hear them speak for themselves, as I would want if it were me defending my faith at the point of a sword.

And isn't murder in the name of Jesus a heresy too? I am having trouble finding the high moral ground here, considering Jesus' explcit rejection of the use of lethal coercion on behalf of His kingdom:

Joh 18:36 Jesus answered, My kingdom is not of this world: if my kingdom were of this world, then would my servants fight, that I should not be delivered to the Jews: but now is my kingdom not from hence.

Oh, and one more thought. If they were so set against reproduction, wouldn't they be a self-correcting problem, simply depopulating themselves into historical oblivion? Would not the approach of Gamaliel have been more appropriate, more resigned to the infallible sovereignty of God than the fallible arm of human flesh? Something doesn't add up here.

Peace,