Didn't wipe out the Essenes. Didn't wipe out the Galileans. Both of which were unique groups with non Judeaic theology and cultural norms. Even when Peter dealing with the [bless and do not curse][bless and do not curse][bless and do not curse][bless and do not curse] crowing 3 times even when Jesus was on trial and Peter denied Jesus, those around him recognized him as a Galilean and not a Judean.
The Essenes were among the major 3 sects of Judaism. Pharisees, Sadducees, Essenes. The Essenes were not some hippy commune hiding out in the wilderness. They had a presence throughout Israel. The fact they are not really mentioned in the NT, is that they are the closest aligned with 1st century Christianity than the other two groups. The Pharisees and Sadducees were in constant conflict with Yeshua, so their reference comes up more often. John the Baptist and even Yeshua were very familiar with the Essenes.
And Even Josephus mentions the Essenes in 75AD, 94AD, and 97AD. Pliny the Elder even discussed them and their geographic location up to his death in 79AD.
And it was not a rabbi or two that established the Council of Yavne, the Sanhedrin was moved at the destruction of Jerusalem to Yavne and the Sanhedrin was composed of both Saducees and Pharisees. It was there clear up thru the Bar Kochba rebellion of 135AD.