Yes, at first sight it seems crazy, but I think we need to remember that Sayid is fixated on three things:
1) getting off the island;
2) getting everyone else off the island; and
3) getting the hell away from the island.
Now, Ben has never done a thing to help that process along, and furthermore, Ben is with Locke, the guy who blew up the Flame and the sub (allegedly). Now he has a man on the freighter, whose mission seems to be to sabotage everything and possibly even blow it out of the water. So no help there.
The freighties, however, are not particularly friendly, but they are not overtly hostile or aggressive either. They brought Sayid and Desmond off the island, they are not treating them badly. Whatever other agenda they may have, they are still the best hope for getting back to civilisation, but only if Michael can be prevented from destroying the ship first.
In a situation where (it seems) everyone has to take sides, Sayid has clearly aligned himself with the people who seem most likely to get the Losties rescued.
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