I think the big question now is why did Eloise send back Jack & Co. if she knew they wern't supposed to go?
What makes you think they weren't supposed to go?
they weren't, but he was simply referring to his plan to change the future then. As far as the closed loop goes, they're absolutely supposed to be there.
That's why Eloise told Ben it would be bad if he couldn't get them all to go back. In that case it would cause a paradox and destroy the entire universe!
(Granted that's a worst-case scenario. The destruction could be very localized, limited to merely our own galaxy.)