Separation is not negative, like many would have us believe. There's so much talk about unity, love, and oneness within Christianity, that to bring up something like separation is almost like saying a swear word! But, if separating is something that GOD is doing with us, it MUST be good. Not only is it good, but it is holy and righteous. I believe that often when we think of sanctification, we fail to realize that it is true separation. Separation is something that we've been conditioned to shun and avoid by having verses like John 17:21 and Romans 12:5 thrown at us (completely out of context, I might add).
Jesus never promised that the church would be completely unified, and to strive for such unity is to disobey Scripture. You may think that's a strong statement, but it is true. Jesus PRAYED for unity, but that is completely different than PROMISING unity. In fact, when John 17 is interpreted properly within context, it's not talking about some kind of global church unity at all. We see division in the church from the earliest time in the New Testament. Look at Paul's warning in Acts 20. For I have not shunned to declare unto you all the counsel of God.
Take heed therefore unto yourselves, and to all the flock, over the which the Holy Ghost hath made you overseers, to feed the church of God, which he hath purchased with his own blood. For I know this, that after my departing shall grievous wolves enter in among you, not sparing the flock. Also of your own selves shall men arise, speaking perverse things, to draw away disciples after them. (Acts 20:27-30). Such a warning assumes that the church will constantly need to be on guard and separating itself from false teaching. It's just they way things are! Man is sinful, and the devil is continually going to try and corrupt the church, because it is the bride of Christ. We need to be careful.
The Bible tells us of one time when the church will be one. It's in the last days.
Revelation 13:4,6 11-15. And they worshipped the dragon which gave power unto the beast: and they worshipped the beast, saying, Who is like unto the beast? who is able to make war with him? And he opened his mouth in blasphemy against God, to blaspheme his name, and his tabernacle, and them that dwell in heaven. And I beheld another beast coming up out of the earth; and he had two horns like a lamb, and he spake as a dragon. And he exerciseth all the power of the first beast before him, and causeth the earth and them which dwell therein to worship the first beast, whose deadly wound was healed. And he doeth great wonders, so that he maketh fire come down from heaven on the earth in the sight of men, And deceiveth them that dwell on the earth by the means of those miracles which he had power to do in the sight of the beast; saying to them that dwell on the earth, that they should make an image to the beast, which had the wound by a sword, and did live. And he had power to give life unto the image of the beast, that the image of the beast should both speak, and cause that as many as would not worship the image of the beast should be killed.
In light of these verses and other clear teaching in the Bible, the emphasis on "unity" amongst churches today is kind of scary! There's all kinds of dialogue going on between various religious groups and cults, and it can only mean one thing. The return of Christ is very near! That's one reason why I actually like separation. I like churches that have differences in beliefs and are willing to stand for them, even if they are wrong. I may not agree with another denomination's interpretation of the Bible, but I certainly respect them if they are willing to sever some ties in order to hold to what they believe is true. We as Christians shouldn't be afraid of separation. We shouldn't fear differences in denominations or sects. Instead, we should fear what is really troubling. Unity and a one world church! That church is going to be centred around false worship of the beast, and ultimately it's leaders and those deceived by it will receive their judgement in the lake of fire.
One of my favourite promises in the Bible is that God has chosen me to be a set apart (sanctified, separated) person that belongs to Him. My salvation did that for me.
I Peter 2:9-10
But ye are a chosen generation, a royal priesthood, an holy nation, a peculiar people; that ye should shew forth the praises of him who hath called you out of darkness into his marvellous light; Which in time past were not a people, but are now the people of God: which had not obtained mercy, but now have obtained mercy.