You are correct in holding to the fact that all of the scriptures must harmonize.
Some of the Jews that were responsible in wanting Jesus to be crucified were already born again, and those were the ones that Jesus was asking his Father to forgive.
When a person is born again, God transforms them from being spiritually dead in sins (Eph 2:1) to being spiritually alive in Christ with the indwelling of the Holy Spirit.
One part of that transformation is that God exchanges the heart of stone of the natural person(1 Cor 2:14) to a heart of flesh, (Esek 11:19 and 2 Cor 3:3) that can be "pricked" (Acts 2:36-37) to feel guilt about spiritual things.
To show the contrast in their response, when hearing Stephen preach the same accusing sermon (Acts 51-54) that Peter preached on the day of Pentecost, Those natural beings, being cut to the heart, responded by gnashing on Stephen with their teeth.