It would not have been outside the realm of possibility for Dharma to have built a place of worship like a temple for their religious staff members to pray at. Maybe that's why there's a Dharma logo on Ben's map. Or the real temple could simply be close to or next to whatever "church" Dharma may have erected for their team.
Th reason I DO NOT think it's a Dharma station is that it's supposed to be a sanctuary, "the last safe place on the island" from the pesky freighter people who supposedly want to kill everyone on the island once they capture Ben Linus. Widmore's people would most certainly know the location of ALL the Dharma stations on the island therefore, if the Temple was a Dharma station, it would not be a safe place for Ben's people to hide.
Tha's my 2 cents.
Maybe the "Temple" ie "A safe place", is the code name for the location and method they can use to get off the island. (just a wild thought with to much time between shows)
BTW-- How does Locke blowing up the sub fit in with Tom being off the island visiting Michael? Can it be said for sure, the Sub is not destroyed, or not the only way off the island?
-<Or more likely I start