One of the main reasons that the Reformation/Counter-Reformation became so divisive and so deadly is that the leaders of the secular power structure in Europe at the time used the divisions in the Church to further their own secular ambitions.  And of course, many of the Shepherds-in-Chief were part of the Church's power structure and the secular power structure at the same time.  This is something that probably needs to be continually guarded against to this day, if Christianity's institutional brokenness is ever to be repaired.
On the other hand, the Body of Christ probably does not need institutions in order to thrive.