I find it very hard to believe Michael is dead (as the other people on the freighter). There seems to be a big controversy about it. The fates of those on the freighter seem very unclear to me -- it appears they've all exploded with the ship, but the consequences of this make little sense.
If Michael was not "permitted" to blow up the freighter earlier in the voyage, what significance is there in waiting to blow up the freighter with "innocents" on it? Are all the people taken onto the freighter "bad people"? Interesting how the only people who would definitely know that the freighter is blown up are the people on the helicopter. Was this one big set-up by Jacob, to drive them to do certain things in the outside world? Ben's petulant "So?" seems typical of Ben, but maybe there's an underlying message here. Either the freighter people's deaths were meaningless, or part of a greater plan, perhaps?
Something doesn't seem clear here, possibly further explored in S5? I find it hard to believe also that Lost would be sloppy in its exposition of such a major event.