I think the big question now is why did Eloise send back Jack & Co. if she knew they wern't supposed to go? Is she actually a bad guy? Or was she also trying to change the past and possibly save Dan?
Maybe in the original timeline Jack & Co. never returned to the Island, so Dan wen't out to find the Hostiles by himself and got shot. Maybe Eloise hoped that by sending Jack & the rest back that she could change the outcome, but unfortunately she didnt.