You forget that "the story" as you so accurately described it didn't arise until decades after Jesus' death -- exactly like I said.
Mark's Gospel wasn't written until decades later -- where's the problem?
And yet he was still crucified by the Romans in the standard Roman fashion for rebels, traitors, and would-be revolutionaries.
Jews stone; Romans crucify.
No the story (nonfictional to clarify since you seem to need that) had been around from the time of his death as told by the disciples.
“Fellow Israelites, listen to these words! Jesus the Nazarene was a man whose credentials God proved to you through miracles, wonders, and signs, which God performed through him among you. You yourselves know this. In accordance with God’s established plan and foreknowledge, he was betrayed. You, with the help of wicked men, had Jesus killed by nailing him to a cross. God raised him up! God freed him from death’s dreadful grip, since it was impossible for death to hang on to him. David says about him, I foresaw that the Lord was always with me; because he is at my right hand I won’t be shaken. Therefore, my heart was glad and my tongue rejoiced. Moreover, my body will live in hope, because you won’t abandon me to the grave, nor permit your holy one to experience decay. You have shown me the paths of life; your presence will fill me with happiness. “Brothers and sisters, I can speak confidently about the patriarch David. He died and was buried, and his tomb is with us to this very day. Because he was a prophet, he knew that God promised him with a solemn pledge to seat one of his descendants on his throne. Having seen this beforehand, David spoke about the resurrection of Christ, that he wasn’t abandoned to the grave, nor did his body experience decay . This Jesus, God raised up. We are all witnesses to that fact. He was exalted to God’s right side and received from the Father the promised Holy Spirit. He poured out this Spirit, and you are seeing and hearing the results of his having done so.
Acts of the Apostles 2:22-33 CEB
http://bible.com/37/act.2.22-33.CEB
It just wasn't written down until later, but it was taught and preached up until then.
And Jesus was crucified because that's what the Jews demanded. Pilot was going to let Jesus go, but the Jews demanded crucifixion not stoning, so pilot gave in to the Jews demands. By the way it was done fulfilling prophecy.