In regards to leaving the existing institutional system, I have always believed that there is only one right reason to leave the institutional church. That is, it must be from God, even if those still in the institutional church cannot understand you. While reading Manfred Haller's "God's Goal: Christ As All in All" recently, I find that he has addressed this attitude of leaving beautifully by centering it on Christ.
It is not easy for someone hearing God's call to flee Bablyon to actually make the step. No one who is one with the God of the Bible can leave Babylon without being aware of the deep dilemma he puts himself into: On one hand, God demands obedience from us, and distance from the things which oppose His will. On the other hand, we can't renounce those who truly are our brothers, who are part of His body, even if they are comfortable in Babylon and not able to understand what could be so wrong with their churches. How can one take lightly the decision to leave the land of one's fathers? We were all born in Babylon, because Babylonian captivity of the church is already many centuries old. are we not bound with every fiber of our being to that which is precious and holy to the vast majority of christians, a system they live and die for and defend with everything they have?
The one who carelessly renounces his brethren and withdraws from them is not acting under the influence of the Holy Spirit and is not in the will of God. Such a one has not fled Babylon; he has only rearranged the setting somewhat. He is either evading certain personal difficulties because he cannot submit himself, or he has his own goals in mind and does not want to be hindered. But these things have absolutely nothing to do with the restoration and building of God's church. The one who can leave Babylon without paying a price has no idea what God is after.
Personal convictions, doctrines, popular movements, and striving after piety are not reasons enough to leave Babylon. The witness of God, the New Testament church, does not rest on reactions to undesirable circumstances, nor on convictions or matter of theology. The witness of God rests on absolute facts, on spiritual actualities fully independent of our ability to believe them. The foundation of the church is the risen, living, ascended Jesus Christ, exalted as head over all. This person in all the saints is the reality of the church. Whatever we do, wherever we go - we find ourselves in accordance with God's will and outside of Babel only when these absolute facts are the basis of our lives, all our dealings and our fellowship.
This was the foundation the first New Testament churches had (despite all their external diversity). This remains the basis of the restored church returned from Babylon. Separateness and doctrinal fastidiousness can never be the motive for restoring the church of God, but obedience and intercessory return to the original foundation of New Testament reality.