Take a much closer look at the events described in that passage in Numbers. There were those among the Israelites who had consecrated themselves to another God. Then, right in front of everyone there, someone went into the brothel to sleep with a harlot. The children of Israel were the ones weeping at the door of the tent, not the two in the act. That’s why it says:
in the sight of Moses, and of all the children of Israel, who were weeping before the door of the tabernacle.
Then notice it says that :
Phinees …] Went in after the Israelite, into the brothel-house, and thrust both of them through together, to wit, the man and the woman in the genital parts. And the scourge ceased from the children of Israel:
So that verse from Numbers is not about the people being killed for repentance, it’s about two people who were blatantly flaunting their sin being killed in a brothel.
If that is the incident you are speaking of, it did not happen that someone killed two repentant sinners at the entrance to the tabernacle.
The thing is, we are supposed to read these stories not as just a literal story where God demands someones death, but as a lesson for us (one that we must always realize is anthropomorphized to place emotions on God that we can understand.) The lesson here, I believe, is that we must remove from our midst all those things which draw us to sin. Someone said it once that being an alcoholic in AA helps you understand these stories all the more clear. You can’t just ignore the alcohol, you can’t just take it in small doses, you have to kill it… get rid of it… remove it completely from your midst, or you’ll fall back into it. That is the lesson God wants us to learn from these stories. That to get rid of those sins, those things we keep falling into it… it’s not enough to just slow down… not enough to just keep it in the other room, in the brothel away from sight… but rather you gotta get rid of it. Remove it from your life. Kill it. Before it ‘infects’ the rest of you.
(Helpful to check other versions of the bible to see the translations. In the Douay Rheims this is much easier to see than in the NAB, NIV etc. )