It certainly seems that Ben's map was leading them into a trap. I don't believe that Danielle is truly dead, but there's a good chance that Ben saw to it that Karl was taken out. Ben doesn't want Alex to leave the island and if Karl got her pregnant she would be doomed if she stayed, so it makes sense that Ben would make a move to deal with that possibility.
On the other hand, Lapidus apparently flew Keamy to the island. They showed us Keamy's target practice for a reason--either to set us up for an island incursion or as a bit of misdirection so we would think of him rather than Ben as being behind the sniper fire.
Anyway, Michael left the island with Walt in late November and has returned in late December, and I'm having a hard time compressing all of the events of his flashback into a mere month. Giving him time to be rescued and then to meet up with the freighter and sail back to the island, we are only left with about a week or so for him to have a problem with his mom and Walt, get suicidal, heal from the car wreck, etc. Michael's mom confirmed that he returned to NYC after an absence of two months, so island time and NYC time appear to be synching up pretty normally (ruining my theory about Michael jumping into the past upon sailing away from the island on Ben's heading). I don't buy that he would so quickly be ready to kill himself and abandon Walt after such a brief period of trouble after their rescue.
Also, Tom was only off the show for about a week (island time) between the Others leaving the Hydra island in "Stranger in a Strange Land" and him showing up again at the barracks playing football with Jack in "Par Avion." That means that Michael's encounter with Tom in NYC took place about two weeks after he sailed away with Walt in "Live Together, Die Alone." This would have been in the middle of December--hence the Christmas decorations seen in the flashback. So it appears that Michael had only been back in NYC for a week or so at that point and was already ready to write off his relationship with Walt and kill himself.