No I don't think Desmond has met Michael until then cause remember the boat that Des got for the race he got through Libby whom Michael had killed, so if Des had met Libby then he'd be wondering "wtf" kind of like how he is now that he has heard from the captain whose the owner of the freighter.
And since we already I know that Ben will have anybody killed who gets in his way one way or another, maybe he knew that Libby worked for Widmore and that's why Ben had Michael kill her. Not sure if this has been mention before or not cause I hadn't read everything that's been posted.

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Standing in the ocean with the sun burning low in the west
Like a fire in the cavernous darkness at the heart of the beast
With my beliefs and possessions, stopped at the frontier in my chest
At the edge of my country, my back to the sea, looking east