The sects that you refer to were the non-religious and anti-religious groups, who had control of the political offices in the Temple, such as the high-priesthood. However the common people who revered and worshiped in the the temple were the religious Jews who followed the teachings of the Rabbis. The non-religious groups disappeared, they had no long-term staying power and were not interested in keeping up a Jewish facade when there was no longer any power positions for them to occupy. As for your remark about the third temple, it will be built by God after the coming of the Messiah, so it will have God's permanent protection.
You are speaking of the temple mentioned in Ezekiel's prophecies, which comes down from heaven?
There has to be some sort of temple built before then, since there is a false christ that will defile a "holy place" just before the Lord's return.