It would seem to me that he actually shot himself, gave Henry the gun, and then let Henry escape. Then when the group gets there they find Michael injured, Anna dead, and the other girl near dead. Michael will be undone when that other girl (he thinks is dead) is nursed back to health.
That's my take on the ending there. Michael clearly has been manipulated, his child being used as bait, and his rhetoric being used to cause the beach crew to wander into the Others hands.
I did like when Hurley said he was gonna get so drunk he'd remember where he knew the girl from and she looked scared. "oh that's right, we know each other because we were both crazy... how exactly are you a shrink???"
Does it seem to anyone else that Jack's dad is a super major player in this whole mystery. A doctor with more going on than anybody knows about with connections all over the world and seems to have been in a position to know everyone on that airplane.
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Yes I agree he Shot himself, and then probably killed the Other they had in prisioner and made it seem like it was self defense.