Gamaliel, a member of the Sanhedrin and a renowned teacher, considered it possible that Jesus and His disciples were from God (see Acts 5:39). He knew too that if they weren't, they would destroy themselves (Acts 5:38), and so he concluded that the early Church should be left alone (Acts 5:38).
The Sanhedrin apparently accepted Gamaliel's advice (Acts 5:39). However, this is confusing because they had the apostles whipped, which doesn't seem like letting them alone (Acts 5:40). This confused response to Gamaliel's advice may indicate that his advice was confused. If Jesus and His disciples really came from God, they would not be merely legitimate but the beginning of the greatest of God's works, for Jesus claimed to be God incarnate. Also, if Jesus and His disciples were not of God, they were not so harmless that they should be ignored. They were claiming to be the fulfillment of Joel's prophecy that the Spirit would be poured out on all mankind (Acts 2:17; Jl 3:1ff). Moreover, the early Church maintained that we had murdered God (Acts 5:30), that He had risen from the dead, and that He would judge us (Acts 10:42) and raise us also from the dead. With such a revolutionary message, the early Church was hardly harmless. The early Church was to be joined as soon as possible or exterminated immediately before it did even greater harm.
How does this compare with the Church today?