I think it's much more likely she is a weird loner survivalist then one of the others or DHARMA. The reason she didn't want to go into the house was because she really fears the Others, so much that she has done everything to avoid any contact with them. And really, Sayid was shot straight away so she was right.

Her methods seem a bit weird, to keep to herself all these years, avoiding the Hostiles at all costs, paranoid etc. But I think it's more probable that she is a lone survivor and somewhat derranged then to believe that EVERYTHING, literally EVERYTHING she's told us is a lie. She's already mysterious enough without it ALL being a cover.