I have always been a staunch Jacob supporter no matter what they threw my way on the episodes. However, this is the first episode that made me start to question this. Jacob told Richard that the island was the quark that was keeping the MIB from escaping. However, in the alternate timeline the island has sunk! Therefore no quark holding MIB back. And in my opinion everything in the alternate timeline is a lot better for everyone then in the original timeline.
The only shred of hope I am holding on to is perhaps MIB died when the island sunk.