Not so, in the early years, even when the apostles were still alive, they tolerated those in the congregation that caused divisions. Paul drew the conclusions of such men based on their fruitage which coincided with Jesus' words that "by their fruits you shall know them". Yes Paul did warn Timothy about Hymenaeus, Alexander, and Philetus in the congregation, but even he didn't remove them, just gave them a scathing review and told people to avoid them. (1 Ti 1:18-20; 2 Ti 2:14-21)
John wrote in his third letter about Diotrephes and described his conduct as being ambitious, proud, rebellious, disrespectful of apostolic authority, and inhospitable. John also added that Diotrephes tried to hinder those desiring to show hospitality to the brothers and to expel these from the congregation. Yet this wicked man was allowed in their midst and had the ability to interact with them at their meetings. In contrast to him, John highlights the goodness of Demetrius to show the dichotomy between the two.
Similar to Diotrephes, we have another example, Satan the Devil. Just like Diotrephes, Satan too is ambitious, proud, rebellious, disrespectful, and inhospitable. Yet, he was allowed to come and go as he pleased from heaven to earth all the way until recently. Up until that point, he could interact with the congregation of Jehovah's angels as he saw fit. This was highlighted in the book of Job where, on two occasions when Jehovah was holding an assembly, Satan strolled right in with the rest of God's angels and proceeded to discuss his plans against Job. (Job 1:6,7; 2:1,2) Here is a being that has caused all of this turmoil to the person of Jehovah and yet God still tolerated his wickedness. Until Jehovah was ready to remove Satan and start His countdown to Armageddon, Satan was allowed to interact with any and all in attendance and come and go as he wanted.
And lastly, in keeping with tolerating wicked men in their midst, Jesus set the same example as his Father. How long did he let Judas remain in his presence even though he knew him to be the one to betray him? Even the other apostles knew he was a thief. (John 12:6)
Paul was concerned about "ravenous wolves" entering the congregation when the apostles were gone but knew they would show up regardless. The most he could do was warn them to look for their fruitage. This is also the very reason why shunning and disfellowshipping is a sin.