Referring to Lostpedia for The Temple: Ben said it's 1.5 days walk from the Barracks, and a map showed it to the northwest. This would not put it in Dark Territory. Of course sometimes they give directions that seem to indicate the Swan is on the north side and the Barracks are on the south side of the Island, inverting the blast door map. That always confused me.
Also interesting, Alpert and Others were there for sanctuary in S4. Ben sent Alex and Rousseau there for safety in S4, but the Losties weren't allowed in for some reason. Ben said it's "not for them".
Is this because Cerebus is in the Temple and would kill them if they went in there? Or because they would get the "sickness" and become brainwashed Cerebus acolytes like the Frenchies?