If the passengers of 815 are dead, yet Michael and Walt were allowed to leave the island, where did they go?
Well they obviously aren't dead in this timeline, the one we are watching, otherwise we wouldn't be watching them! If Michael and Walt were allowed to leave, and they didn't die, then I beleive they are back in the real world, or another timeline of the real world, and that this will have major consequences in upcoming episodes.
If the crash of 815 was staged, how did anyone get Michael to keep his mouth shut about their ordeal? Michael would find a way to blab with his head cut off.
I agree, and this may be what triggered Naomi to the island. Everyone thinks it's Penny and her Portugeuse friends locating a mysterious magnetic anomaly (how would you located one, anyway?), but it would be cool if Michael has sent "help".
If Michael and Walt were sent to their deaths on that boat, how did Ben maintain control of his pride after they saw him break his word?
If they were sent to their death, this may be one of the reasons Ben has lost touch with the island, and why he became sick, because he is no longer "a good person".
If Michael and Walt entered a separate reality, was this one that occurred with no plane flight?
Wow, I just got a head rush.

If Naomi is lying, why would she lie? What outside group would want the castaways to believe that they had nowhere else to go....this was it? (I believe that Dharma still exists and Naomi is a member. That is why Mikail was looking for her).
I don't believe she is lying either, she may in fact be Dharma, even if she is working for Penny she may still be a Dharma holdout. However, if she is (and Michael has not told the world of 815's fate), since she has no connection to flight 815, nor has any prior knowledge of them being there (she's supposedly looking for Desmond), then it would seem to make sense that she is telling the truth.
Bottom line, as always with Lost, we just don't have enough information to make an inference at this time. Check back after Season 4 is over.