Why do you think the Gnostics, Cather's, Marcionites and other groups disappeared as well as all of the pagan religions of Europe.
What happened to all of the "pagan" religions that died out under the "pagans"? Were they all persecuted into non-existence? Do you seriously think the only way a culture can disappear is via systematic eradication?
99.9% of all belief systems in history have disappeared. Christianity had reduced massively in Europe over the past century, is this purely due to systematic persecution?
But your whole argument is based on an error. Gnostics didn't 'disappear'. If you accept that the Cathars existed (which many historians don't, but that's another story), you accept there were thriving Gnostic sects in Northern Europe nearly 1000 years after the almighty Church began their relentless persecution of them.
Marcionites lasted the best part of a millennium too. Pagans likewise, if not longer.
Hardly great support for your 'omnipotent' Church hypothesis.
Honestly though, try to understand the logistic of running an ancient empire and how institutions functioned in the ancient era. Then you will understand why it's naive to overstate their ability to project centralised power.
Roman Emperors couldn't even make people comply with edicts and they were frequently ignored. Why do you think the Church could control the Empire at will?