I think that most people are missing the fact that Desmond was offered a job by Widmore in the first time we saw them interact on the show. When Desmond went to his office to ask to marry Penny and Widmore thought he came looking for a job...and the whole "Great Man" conversation. Maybe Desmond did go to Widmore's office but not to ask permission for marrying Penny but to simply get a job. Desmond works hard and becomes Widmore's right hand man. I know this is probably irrelevant to the show's plot but it is just something that falls under differences between two timelines.