I have just had a dark, and horrible thought. But don't write it off just yet.. after all.. this is Lost. What if it is not just Eloise, Widmore, and Faraday who have manipulated Desmonds path. What if Penny is in on the secret too?
Think about this one fractured family for a second. Eloise and Widmore, once lovers, create Faraday. Some years later, Widmore apparently fathers Penny to a different mother, making Daniel Faraday and Penny half-siblings. Eloise has convinced/manipulated Desmond during his lifetime, notably in the episode "Flashes before your eyes", convincing Desmond to run from Penny and go to the island. In "The Constant", Faraday convinces Desmond to go to Oxford and deliver the younger Faraday a vital message, key to his research. In "The Package", Widmore has kidnapped Desmond and clearly has big plans for him, so we know all these three have had impacts on Desmonds lives, and have needed to use him for purposes related to the island. There seems to be a grand purpose as to why these three need to use Desmond, as if Desmond is uniquely special and only Desmond can help in certain situations.
But could Penny be on this grand scheme? What if she is not as estranged from her father as we believe her to be? We obviously need to ask ourselves why would Penny create such a facade, and go as far as to have a child with him. Well in the first instance, perhaps Widmore deliberately asked Penny to create a facade of love with Desmond to give something Desmond to hold onto, while he was alone in the hatch, to make sure Desmond had someone to love. After all, it was Penny's "love" that saved Desmond, and provided him with the faith/hope to turn the failsafe. But as Christian was said to Jack, "Even if it's false hope, it's still hope". Desmond didn't know it was false hope, to him it was pure love.
From this moment of turning the failsafe, was it really Penny searching for Desmond with her own team of Portuguese sailors? Or was this all funded by Widmore, under the guise of Penny's enduring love. Think of the amount of times Widmore has tried to use a vessel to gain access to the island. The Freighter, The Submarine, is it such a stretch to imagine that Widmore funded Penny's search team? Under the guise of the trusting Penny, this not only allows Widmore access to all of Desmonds whereabouts, but als, for a brief time, meant that the Oceanic 6 were onboard Penny's (ie. Widmores) boat, giving further information to Widmore. And information = power.
Flashforward to current events. How did Widmore so easily gain access to Desmond? Easy - Penny has been keeping tabs on Desmond and has let her father know where Desmond is. She knows that stopping the Man in Black is going to save the world/universe, so hanging out with Desmond and providing a false love to him is a small price to pay for saving the world. And why did she have his child? Because she knows the child, Charlie, will also possess Desmonds time travelling powers.
In closing, if we go back to that moment in "The Constant", where Desmond is about to black-out, Widmore mysteriously says to him, "It's not me who hates you Desmond". No, it's not Widmore who hates Desmond. It's Penny. Penny has been doing this one, long, tough job for her father, and has grown to resent Desmond.... But she does it because she is doing her part to save the world.