SO bear with me on this because I have the ideas in my head but am having trouble putting them into word...
What if Daniel is the MIB and Desmond is Jacob? Eloise clearly knows something is going, which is shown during her talk with Desmond in the FST. And when the MIB was talking to Kate, he had said that he had a crazy mother that made him that way due to some sort of "unfortunate incidents" or something along those lines. Well if you remember, when Daniel was shot by his mother during his time traveing, he looked at her and said, "You knew," as in, Eloise knew that by pushing Daniel to go to the island it would lead to her killing him in the past. Kinda sounds crazy for a mother to want to kill her own son.
And as for Desmond, Whidmore said that he's going to ask him to make a sacrifice, and what's a bigger sacrifice than spending the rest of your life (maybe eternity) by yourself protecting a mysterious island?
And one last note: Penny is still Daniel's half-sister in the FST, so Eloise was cool with Whidmore fooling around like Tiger Woods?
Like I said, bear with me on this, and if anyone can add to this / make it clearer, please do.