I've been meaning to post a link to that theory all week, you beat me to it!
But in all seriousness if you haven't checked out the rest of that site (lost-theories.com) do so, it has some really cool theories.
I don't think that Miles is Ben's "man on the boat" because 1. there's still sabotage occurring even after Miles has left the boat and 2. Ben told Miles that he had a man on his boat, which would be kind of wierd if Miles was his man on his (Miles') boat have I got you confused yet? lol. I do think there is definately more to the "3.2 million dollar conversation" than meets the eye though. The instant Miles let on to Ben that he could be bribed I was thinking "Wait a second, Miles travelled halfway across the world as a member of an elite team recruited by some mysterious man for a top-secret mission and he's saying he can be bought out for $3.2 million? That doesn't make sense!". It seems to me that whoever hired Miles could offer him more than a measley $3.2 million (yeah I know it's not measley, but when you're dealing with people like Dharma or Hanso or Widmore or the likes of Abbadon it is). Miles also knows that there's no way Ben could get him money anyway, and if Ben was indeed powerful enough to get Ben money from his current position wouldn't he also be powerful enough to get more than $3.2 million?
Anyway, the whole conversation just seemed so staged and fake that it has to be. I guess the real question than is this: What is the true relationship between Miles and Ben?