So when Jesus said the church would be killed for His sake, Paul went behind the back of Jesus and prevented that from happening?
You make no sense.
You do not understand the dynamics that were in operation throughout those early centuries. The church was persecuted first by the Jews, aka Saul. Then pagan Rome came to the party and continued those (satanic) attacks for centuries. What was the effect on the church at that time? It grew strong, and through the grace of God, those persecutions resulted in the church turning the world upside down. Those persecutions and open war against the true faith prompted the believers to draw closer to Christ, and through His power they overcame all opposition and spread the gospel to all the world, even to the point where Constantine, in order to preserve the Empire, 'became' a Christian, and declared Christianity the official religion of the Empire. Up to this point, Satan had been utterly failing in his war against the church. So he decided to change his focus and direction. He couldn't destroy the church through violence, so he chose to use deception.
Constantine's so called conversion was the beginning of this. The persecutions against Christians ceased, at least for the time being. But what was just around the corner was far worse. And God knew this, which is why Jesus repeatedly warned the church to let "no man deceive you". Yes, Jesus warned against persecution, but only a couple of times. The real danger was coming in the form of compromise and deception. Hence His allowing pagan Rome to continue in power until such time as the church around the world was in such a state of preparation as to recognise compromise and deception when it came.
So when pagan Rome fell, in the 5th century, and the church rose to political power in Rome, calling itself 'Catholic', and introducing all manner of wrong doctrine and errors and pagan symbolism in order to appease and make things easy for the pagans to feel "comfortable" in calling themselves Christian, the church outside of Rome such as in Asia, Britain, southern France, northern Italy, and the far East, resisted the changes and compromises to truth, recognising the papacy as the Antichrist of scripture and the man of sin, and resisted his self proclaimed authority over their spiritual destiny.
If God can use a donkey and speak through that animal to censure his prophet, He can use a pagan nation to protect His church.
So yes, the historic situation over those centuries previously followed the prophetic picture. And all the early church fathers recognised this, as they knew the times in which they lived. They could see the desolations that the barbarian tribes were bringing down upon the Empire, and those ECFs themselves were warning the church that soon a greater enemy would arise. And some of them were subsequently deceived and unknowingly became a part of the very system they were warning against.