I think Walt is THE MAN on the boat working for Ben. I also think Michael is on the freighter but not workinig for Ben. When Ben kidnapped Walt that is when they could have set up the plans for Walt to work for Ben. When Ben told Michael which direction to leave the island he was sending them right to the freighter. The twist will be that we will assume it is Michael working for Ben when we see him on the boat but it is really Walt who is Ben's contact.
This is the theory that I'm buying. Walt was being held for quite some time before being given back to Michael. Adding the time with the Others (including his time spent being entertained in Room 23) and his unique abilities would lead me to believe that he'd be of the greatest use to Ben. He's also young and impressionable which makes him great fodder for Ben.. perfect subject to brainwash into believing that the people on the freighter are the bad guys and Walt needs to help his friends who are on the island. Walt's psyhic abilities (or whatever they are) would explain his ability to be able to communicate with Ben and provide information. IMO, Michael's involvement in the operation would be limited to getting Walt onto the freighter.
I think Michael is too obstinant to go along with anything Ben wants... he'd only help if his son's life was in danger which it isn't (so far as we know anyway).
I also don't believe that Michael being Ben's man on the boat would shock Locke but Walt definitely would. Locke and Walt had a relationship while most of Michael's relationship with Locke was restricted to his distrust of Locke and his wanting to keep him away from his son.