The Historical record is what it is. It was your sect that first merged with the state and then used the power of the state to persecute Christians. It took about 1200 for the Reformers to catch up to your example.
That is nonsense. The earliest Church, before it had any associations with the state authorities, was fighting heresies and heretics tooth and nail at the cost of exposing themselves and their own persecution. Obviously you are not familiar with the writings of the Apostolic and Church Fathers of the 2nd and 3rd centuries directed specifically against Heresies, against deviant or deformed Christians.
I think you need to read up on your history. First of all, at the beginning of the Dark Ages (in the Western half of the Roman Empire), there WAS no "secular" power. Rome fell and the only organized unit left was the Church. If you care to read the Church history into the second millenium, they had always fought against investiture (secular princes appointing bishops). However, as you can imagine, the Church didn't have a huge army to conquer people by force. Often times, they had to threaten with interdictions and such. Really, if you were the Pope and you wanted to maintain the authority to appoint proper bishops, what would YOU have done if some prince in Savoy decided to appoint his nephew to the position? I think you are being a bit anachronistic and not taking into consideration the situation faced by the Church.
That the State and the Church "united" only says that they often shared common goals. However, they were constantly vying for the "will of the people". The Church was trying to win souls for God, while the state was trying to win power for itself. Often, these goals were the same because society was so intertwined. Religion was STILL part of public life. Thus, a heretic was condemned by BOTH state and the Church, not because the state was the Church and vice versus, but because both sides saw their positions threatened by particular heresies - by nature, heresy stirred the people to rebel against both state and church. Naturally, then, they shared a common interest in keeping the peace. But it certainly does not mean that even during these moments, that they were still not battling over investiture or simony.
I think a study of the English Reformation would be beneficial to you. That is a perfect example of how the "state" suppressed the Church when given the opportunity. Money and land was in large part the motivating force behind much of the Protestant Reformation. Princes and barons didn't care about such things as "salvation by faith alone". They cared about the ensuing land grab once they saw the opportunity to take control of Church property. Now, what is the excuse of the Protestant Reformation's killing of priests and nuns? Were they trying to suppress heresy, or were they trying to secure their position to maintain their usurpation of Church wealth? Perhaps both, in their minds. But when given the opportunity, it appears that when men get into power, power can corrupt, whether Catholic or Protestant.
Thus, it is false to blame this on the Catholic Church. When given the opportunity, heretics persecuted men of the Church, as well. Ask your friendly Orthodox man. Read up on Church history. Many of the saints were jailed, suppressed, tortured, or exiled. Heretics were certainly not shy in using their power to force their will and interpretations on the people - and when the Church tried to teach the Gospel, they were subsequently silenced. Read the history of St. John Chrysostom, or St. Maximus the Confessor, or numerous other men.
Regards