I'm embarassed to say there's a big chunk of vol 2 of the Institutes I've never read, so I'm working through some of it this week. It's book 4, on the church. I'm skipping most of the refutations of Roman Catholic abuses but enjoying the stuff that more positively sets forth Calvin's theology of the church and the pastorate.
It's interesting to me that in the first several sections Calvin addresses what to do when there are pervasive evidences of sinfulness, even willful sinfulness, in the church. In light of his disgust with Rome, I expected an emphasis on the necessity of separation for the sake of the church's purity. But Calvin repeatedly underscores just the opposite: the need to stay together, united, and to bring to remembrance time and again the need for forgiveness of sins (4.1). I think this was in response to the Anabaptists, who urged separation and an unhealthy demand for what Calvin calls "perfection."
Along this line, here's a statement from 4.1.21 concerning the need for the gospel after, as well as in, conversion. This comes as he defends his point that sin must not overly quickly trigger separation, but rather enjoyment of communal forgiveness among he saints.
"Not only does the Lord through forgiveness of sins receive and adopt us once for all into the church, but through the same means he preserves and protects us there. For what would be the use of providing a pardon for us that was destined to be of no use? Every godly man is his own witness that the Lord's mercy, if it were graanted only once, would be void and illusory, since each is quite aware throughout his life of the many infirmities that need God's mercy."