We should be very grieved that the Church is torn by internal divisions as evidenced by thousands upon thousands of denominations in Protestantism, but it is better that some shall separate themselves from the ungodly and be united to Christ their Head, than that all should agree in despising God.
If we have to fight against godless teachings, then, even if it is necessary to move heaven and earth, we must persevere, nevertheless in the struggle. We must certainly make it our primary concern to see that the truth of God is maintained w/o any controversy; but if unbelievers resist, we must struggle against them, and we must not be afraid that we will be blamed for the disturbances.
For the peace, of which rebellion against God is the token, is an accursed thing; whereas the struggles, which are necessary for the defence of the Kingdom of Christ, are blessed.
Paraphrase from Calvin
Commentary on Jn. 10:19 / I Cor. 14:33