It seems to me that the Man in Black knew about the flashsideways world. I think this is why he was make promises to people, such as telling Sayid he can see his love again, and Claire would have Aaron again, and so on. Because in the flashsideways world these wishes came true, even though it was after death.
That being said, I always thought that Eloise's behavior in the flashsideways world was very odd. It was apparent that she wanted to stay in the sideways with Daniel, the son she essentially sacrificed to the island by sending him there purposely knowing that she would in fact kill him. But it was what she said to Desmond that was weird. She insists that Desmond waking everyone up was a violation. A violation of what? I think, I violation of a deal she made.
Eloise made a deal with the man in black. Just like Claire & Sayid did. And the flashsideways was a fulfillment of that deal. I think she agreed to help the man in black complete his loophole. When Locke saw Christian (who was really the man in black) near the frozen donkey wheel, he was told to find Eloise to come back to the island. And Eloise is the one who told Ben & company to bring Locke's dead body back to the island, which is what the man in black used to trick Ben into killing Jacob.
I think Eloise blamed Jacob for what she had to do to Daniel, even though it was all for the good of the island, so she agreed to help the man in black kill Jacob and in return he allowed her to be with Daniel in the afterlife.
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