To tell you the truth, I am kind of surprised at the lack of responses from your fellow EO's on this topic. It's kind of weird that although your question was addressed to EO's, only OO's responded. It could be everyone is just too busy recovering from the holidays. I know I'm still reeling. It's like I need a vacation to get over my vacation.
I wouldn't let this issue shake your faith in your Church. My priest is always saying that although the Church is perfect, the people who run it are deeply flawed. I think God lets us make mistakes, but eventually draws us back to the truth.
I personally think that is what happened with the EO Church and Chalcedon. I'm one of those people who subscribe to the belief that Chalcedon was originally Nestorian in bent, but that this was corrected by Constantinople II. (For ease of reference I like to call that council "the fifth council," even though my Church doesn't recognize it.) The reason I believe this, is that the historical evidence supports the idea that there was a change during the time of the fifth council. This has been discussed extensively in other threads. The evidence includes such things as Chalcedon being supported before the fifth council by groups and churches which were blatantly Nestorian, but after the fifth council they all went into schism. Also, the four Chalcedonian Eastern Patriarchs, as well as the Pope all initially refused to support the fifth council on the grounds that it contradicted Chalcedon, etc. The fifth council, however, ended up being accepted and it eliminated the Nestorian interpretation which had previously prevailed.
As I said, I wouldn't let this shake your faith in your Church. Again, every church will have flawed leaders who try to lead the people into one direction or another, but in Orthodoxy, God eventually leads us back to the truth.
One thing that has led me to believe that both the EO's and the OO's are the true Church, is how much we have in common after so many centuries of separation. Think about it. For over a thousand years, especially after Islam took over the Middle East, the EO's and OO's have been almost completely out of touch with each other. We have been separated geographically, politically and theologically. And yet, when the 20th century came and suddenly our leaders were able to communicate with each other (because of modern technology as well as diaspora) they found that there were really no differences between us. Our liturgies, though superficially different, were really the same. Our beliefs, practices and rituals were all basically the same. Even our Christology, to the surprise of many, was the same. When all the EO and OO theologians got together, they found that despite the different language, we really mean the same thing about who Christ is.
How could this happen without the Holy Spirit? This is really humanly impossible. The only way the EO's and OO's could be so much the same after so many centuries, is if the Holy Spirit were working in both bodies.
Contrast this, for example, with all the Protestant churches in Europe and America. They have had constant contact with each other, and yet they are all very different in beliefs and practices. So many Protestant movements have come and gone, disappearing after only a few generations, or splitting up into different bodies. That is, in my opinion, what happens when a church is led only by men, and not God.
So don't doubt your Church. It may have, like all churches, had some leaders who were less than perfect, but I believe God has preserved it in true Orthodoxy. The Chalcedonian issue, I think, is almost a red herring, leading the Orthodox people into contention and anger, when we really should be thinking of unity. I am not saying it is not important. It is just that I think we should be spending our time and energy trying to think of ways of realizing here on earth the unity that God seems to have preserved for us spiritually. Let us all pray for the day when we are all (EO and OO) fully reunited with each other!