Tolerating sin and falsehood in the church is something that we cannot do, and if we do, we put ourselves at risk of being disciplined by the Lord. Here's what Jesus said to the church at Pergamum, after having encouraged them for their faithfulness:
But I have a few things against you: you have some there who hold the teaching of Balaam, who taught Balak to put a stumbling block before the sons of Israel, so that they might eat food sacrificed to idols and practice sexual immorality. So also you have some who hold the teaching of the Nicolaitans. Therefore repent. If not, I will come to you soon and war against them with the sword of my mouth. (Revelation 2:14-16)
So, Jesus had some issues with this church. There were some there who held the teaching of Balaam (v. 14). We don't know exactly what was being taught here. But what we do know is that Balaam was a prophet who advised Israel's enemies to seduce the Israelites into idolatry and sexual immorality. That's likely what some of the people in the church were doing.
Not only that but there were others who held to the teaching of the Nicolaitans. We saw this earlier in Christ's message to the church at Ephesus. There are a few ideas on what this teaching was, but it was probably some sort of heresy that led to antinomianism (the idea that Christians don't have to follow God's moral law) and compromise with the pagan culture around them.
Because of this tolerance of sin and falsehood in the church, Christ called them to repent. And He warned them that if they didn't, He would come to them soon and war against them.
How is it that Christ would war against His own church? Remember that this book is full of symbolism, with warfare being a common theme. It's almost as if He's saying, "If you don't stop fraternizing with the enemy, then I'm going to treat you like the enemy." Ultimately, we know that Christ's people can never be snatched out of His hand. But we also know that a visible local church can be decimated by sin and God's loving discipline.
We need to ask ourselves, "Do we tolerate sin or falsehood in the church?" We should always be gracious and kind. But we should never hide behind grace and kindness in order to avoid dealing with sin and falsehood in the church. Christ has prescribed for us exactly what to do when there's sin in the church (Matthew 18; 1 Corinthians 5). Certainly, that includes heresy. And He has also told us to speak the truth in love and that such love-laden truth-speaking is exactly what will cause a church to grow (Ephesians 4). But if that is not happening in a local church, then the opposite will happen: spiritual decay and Christ's loving judgment.
This is why we take biblical doctrine and biblical discipline seriously. If we fraternize with the enemy, our Commander will dissolve and discipline our unit. Praise Him that He is merciful and kind to warn us and to help us to stand for truth.