Since all three references you cite are from the Tanakh -- Jewish scriptures -- why not ask Jews to rationalize?

I think it is all contradictory BS. Don't follow anything in the Bible except "Do unto others..."

It's obvious from the verses in De. 22 that it was not a rape but simple fornication since she didn't scream or cry out. So they were just executing people who fornicated, both parties being guilty. The Jer. verses are about a judgment prophecy, saying that whoever would be doing the killing wouldn't be able to hold back form carrying out God's judgment, that even the Babylonian king would follow out his purpose to destroy the nations he had condemned. It's not saying individual people had to kill. These verses are just a greater detailed telling of what is in chapter 25 of the same book. In Deut. 13 (actually chapters 12-16, were all about religion and worship and how to keep it clean. Their instruction on what to do to other people had to do with moving into the land that God had given them and the people that had false idols and insisted on worshiping them, were to be cleared from this land that belonged to the Jews, not Christians. It was a protection for the Jews to keep them from being contaminated by false religion. Cities of Israel that turned apostate were to be devoted to destruction, and nothing was to be preserved for personal benefit by anyone. The city was never to be rebuilt.