First, the Church is composed of bad and good people. Some of the bad people are outright ungodly and, according to Jesus promise in Revelation, they will be "vomitted" out of His body in the Second Coming.
Anyway, I think that ecclesiologies that tend to identify the Church with the "good" people only have missed an important aspect of what our Lord Jesus Christ came to do. Likewise, bishopocentric ecclesiologies err on the excessive focus on one important, but one only, element of the Church.
The Church is the group of people in whom the energy of salvation, the "Kingdom", dwell, changing their nature of sin, if they confess Jesus Christ, into a nature of Glory. This Divine Energy, which is God Himself, acts from inside these people.
There are many good and holier people outside the Church. But this energy showers over and around them, many times, "reflecting" onto the people around them, but it does not come from within. St. Francis was far closer to the Sun of Justice than the vast majority of people, including Orthodox people. The light was all around him, and yet, it was not *in* him. When a member of the Body of Christ comes near Him, the light shines from within. He is not like a bright mirror reflecting the sun from nearby, but like a small star himself. Even the bad Orthodox have this potential, although they don't "activate" it because they do not confess Jesus Christ in their hearts and don't truly accept Him. They are like sad aborted stars, the soil of rocks wherein the seeds start to grow but are chocked by a heart of stone.
This qualitative difference is the most important one. The differences in dogmas, practices and organization are all consequence of this.