I have always believed that despite outward appearances, the character and behavior of Eloise was driven by her love for Daniel. I never believed that she sent him to the Island to be killed (by her) for the good of the Island. And I think in the FS we see this is true. I think every instruction she has given to Desmond - including the latest admonition regarding Penny - is to keep Daniel alive. Eloise knows that Desmond is Daniel's constant, and she needs Desmond to stay on the path that will protect her son. I don't think she wants to keep Desmond and Penny apart necessarily, as long as their coupling will not interfere with Daniel living. Unfortunately, it is my gut feeling that he will die anyway.
I also believe that the character Eloise is named for the heroine in Alexander Pope's poem Eloisa to Abelard. This poem contains the line "Eternal Sunshine of the Spotless Mind". The poem speaks about divine love and erasing one's memories (and hope), if that love can not be achieved. I believe this ties in with what is going on between Jacob and MiB. Jacob believes that as long as there is hope for divine love, humans can always work towards that goal. MiB on the other hand sees hope as cruel, and wants to put an end to it by erasing free will and replacing it with destiny. With only one path to follow, there can never be hope of changing it. And therefore, there can never be disappointment.