I'm halfway through Season 6 on my first rewatch (I watched the original airing) and I just can't figure out why it is that I'm supposed to think the Man in Black/Smoke Monster is so bad. It's clear that his main goal is to leave the island, but everybody seems to be in agreement that this will have catastrophic consequences despite nobody explicitly stating why.

At this point (we just finished Ab Aeterno), it seems like the only two reasons are 1. that Jacob says it will be bad if he leaves and 2. MiB has a generally bad reputation due to the fact that he's killed a bunch of people. The first reason doesn't seem very compelling to me, since Jacob seems to make habit of regularly misleading people and most of them have realized this at this point in the show. The second reason also doesn't do it for me, since if there's one thing this show teaches it's that we're all sinners, and both sides at this point have slaughtered many, many people. MiB seems to have killed no more innocents than Jacob's side has.

So, why should I not be feeling perfectly okay with MiB being allowed to leave the island, thus effectively removing all conflict from the show during the middle of Season 6? This seems like a major flaw in the plot to me.