What does it mean for a Christian to be separated? We could say a lot about what we, as Christians, out to be separated from, false teaching, immorality and such like. But what we are separated from is only part of true Biblical separation. Many people have derived the name Pharisee from the Hebrew pharez, to separate. The Pharisees were separatists, they separated from all sorts of things - and finally they separated themselves from Christ and from salvation. A purely negative view of separation will lead there, to Pharisees going to hell in their own very religious clique - without Christ.
Biblical separation includes a positive element, and that positive element must be emphasised unless we want either to drive people away, or to make people into Pharisees. The positive element of separation is this - that separation is not end end in itself, but rather it is a preparation for service.
Separation is not end end in itself. We must be so careful in our Evangelical and Reformed Churches never to be fooled into thinking this way, that once we have separated from error we are all fine. Still less should we always be narrowing the circle, looking for more and more people to separate from. In fact I would go so far as to say that we ought not to be looking for people to separate from at all. What we need to separate from are false teachings, and so we separate from the people who teach them, not because of the man, but because of the doctrine! Satan is tempting us to think that, once we have borne a witness by separating, everything is fine. It isn't.
Separation is for service. We separate from false teaching to better bear witness to the truth. Let me illustrate. Suppose that I am in a church where there are two pastors, one of whom is evangelical, the other liberal. Well, the message of that church will be confused, the watching world will not be able to work out what it is actually teaching. If the evangelical pastor separates from the liberal, then his church will bear a consistent witness.
This is the whole point of separation. It therefore follows that we are only to separate from false doctrine, and from gross immorality. We are to separate only over the issue of the Gospel, which does not include Church government or the proper subjects of baptism. My own church has elders who actually differ on these matters. We are, however, all united on the Gospel, Jesus Christ as the propitiation for sins. We separate for the sake of the Gospel, and fo no other reason.