It's a refuge for the Others. They are scattered all over the island but in a case of emergency they all summon in this place to be protected from Smokey. It was mentioned more than a few times in the earlier seasons. Alex, Rousseau, and Karl were on there way to the temple when they were ambushed by Keamy and his men. The Temple is now most likely deserted because of the others joining the MIB and Dogen being killed, the defilement of the spring, and ther massacre at the temple.