John 16:1-4 MKJV I have spoken these things to you so that you should not be offended. (2) They shall put you out of the synagogue. But an hour is coming that everyone who kills you will think that he bears God service. (3) And they will do these things to you because they have not known the Father nor Me. (4) But I have told you these things so that when the hour shall come you may remember that I told you of them. And I did not say these things to you at the beginning because I was with you.
The religious who think they bear God service - will throw the apostles out of the synagogue and even kill them. And the disciples are not to be offended, stumbled or surprised!
The Spirit-filled Christian is an offense to the carnal religionist or the worldly system of official dogma. No system can encompass the Spirit which , like the wind, "listeth where it will" .
It is not atheists, but self-proclaimed religious experts, that killed the apostles and crucified Christ. And as Jesus said they "have not known the Father or Me". They only knew their dogma, their rules and their power.
Now we need truth, and the essential doctrines of the faith are not up for grabs, indeed doctrine is central to the Christian life. But doctrine cannot be a substitute for the Christian life. If we only have doctine - and do not not personally know God, then we can easily become an enemy of true grace.
Systems react to perpetuate themselves and even religious systems can be violent in their antagonism to change. And when the change means the system will come to an end and the Temple be torn down and the priests out of a job and a New Covenant enacted in which they have no place (see Hebrews 9 & 10) then the reactions are very violent indeed!
Jesus wanted the apostles to keep on going even in the face or puzzling, irrational and lethal opposition. Jesus prepared them to face a less than perfect world. A world of evil responses to grace. A world where the one organization that had nurtured their childhood faith - the synangogue, would throw them out and hate them.
Many Christians find themselves rejected by religious systems. One denomination in Australia, a rather liberal one, once refused to ordain me on two grounds a) I was too evangelical and b) I was a bible teacher and "bible-teaching has nothing to do with the ministry of the Word" (their exact statement).
That denomination is now being torn apart by division.
We must remain faithful to Jesus even if it means that our church throws us out. Our loyalty is not to a system but to the Person we know and love who is our Savior.
Now there are some excellent churches, and many where we can be fully Christ's. But if the day comes when a choice between following Christ and belonging to a church must be made, we should know that many have gone before us, and not be stumbled, and choose Christ, without bitterness toward the church, and keep our love of God. For that is what Jesus would want.
Blessings in Jesus,