Jude was writing to warn against professing Christians who perverted the doctrine of grace and rejected the Lordship of Jesus Christ. These men are characterized as vile and godless (Jude 4). It is from these men that we must disassociate.
Consequently, the doctrine that was originally laid out by the apostles is to be pitted against those who preach contradictory doctrine. We have been called to steadfastly maintain the purity of the gospel. In so doing, we must also keep a clean conscience.