I just finished it last night and I felt the exact same way. That one reference from Farley's journal mentions talking C.W. out of his plan- and then the next page is her raging about how much she hates the Mofang and that she wants to survive.

Nothing really felt particularly clear, and all the people here commenting on how unplugging the battery "makes sense" were just acting on a hunch and happened to get lucky. We didn't really know what the battery actually did, where the Tree would take us, or if some other crazy twist would happen anyway. C.W. was pushy, but all the ingame evidence implied he definitely wasn't a bad guy. I personally don't think we got enough of Farley to establish her as the "Good Side" vs C.W.'s "Bad Side." All we really had to go on were a couple holograms and some highlighted words in an admittedly moody, esoteric journal.

I saw destroyed Arizona from Soria, but we're just supposed to infer that just because one tiny middle-of-nowhere area was messed up, the rest of the world was too? Sure it makes sense in retrospect, but it's as you said- it's based on a "hunch" and that kind of annoys me compared to the cut-and-dry ending choices in the Myst games. In those games, getting the "good" ending felt like a logic puzzle in itself based on obvious clues you find in the world.

Maybe I'm just salty that I got the bad ending first, but I thought about it for a while before pulling the plug, and I wasn't able to come to a decisive conclusion either way. In the end it felt like a coin flip to which plan would end up going wrong.