First time poster just found this site and I think its amazing. Sorry if this theory has been thought of already but heres what I think...
I believe the ability to kill Jacob wasn't the only loophole MiB found. MiB was trapped before unable to inhabit a body or human form that wasn't dead. In the first episodes of season 5 it seems as though, the person we thought was John Locke, was experiencing feelings and humanity for the first time in a long time...we thought it was because he had died and come back but I think the real reason was that MiB was able to find his loophole which allowed him to inhabit a body that wasn't dead. Previously he had only been able to inhabit dead bodies and "infect" live ones. The corpse's of the dead bodies he was able to inhabit would disappear, as in the case of Christians. But John Lockes dead corpse and Flocke were together on the beach. In the season 5 finale Jacob says, "Well you found your loophole" to Flocke and Flocke responds "Indeed I did and you have no idea what I've gone through to be here." I interpret that to mean that the loophole is MiB inhabiting a living body. N! ot that he can inhabit any living body but just Lockes because of the loophole.
As to Illana saying he is trapped in that form, it could be because of the fact that now Jacob is dead because when Jacob was alive Flocke was able to show himself as Alex. And "trapped" I think is a bad term cause I think he's now free and WAS BEFORE trapped. This is why Richard is so freaked when he sees Flocke and exclaims, "you...." cause Richard knows of times when MiB had not been trapped and is shocked to see him in a live form.
Which then takes me to the next theory on alliances. I think that Jacob had not been helping Ben over the years but in fact it had been MiB. The reason I think this is that after Ben kills Jacob Flocke says to Ben that Jacob was confused that Ben wanted to kill him. The reason he may have been confused is because MiB had been manipulating Ben for years under his nose. This can be traced back to the cabin.
When Illana comes out of the cabin in season 5 she says that Jacob has not been in there for a long time and someone else had been using it. When John is taken to the cabin with Ben for the first time he doesn't see anyone in the cabin...which fits in with the fact that MiB was unable to take a living form to show himself to all, but Locke does hear him say "help me", which indicates someone was in there. So I think MiB had been manipulating Ben into thinking Jacob was in the cabin when he himself (MiB) was actually in there.
Furthermore, Ben believes that the cabin is really where Jacob is and does not know it has been taken by MiB. We see this in season 4 episode 11 when Ben, Locke, and Hurley visit the cabin again and Ben says that he got sick on the island and that Locke was healed so the Island has chosen Locke and that he (Ben) is no longer chosen. This is why Ben does not go into the cabin but waits and says its Lockes turn to see Jacob alone. Which further shows Ben believes the cabin to be really where people go to see Jacob. This could be viewed as a trick on Ben's part but when Locke comes out and says we need to move the island Ben is all for it, which shows he believed the orders that came from the cabin. When Locke goes inside he sees Christian and Claire who are (widely accepted) to be working with MiB which further enhances the point.
MiB choosing Locke to manipulate fits with Locke's major character flaw shown throughout the show in that he is easily manipulated. So MiB knew he could manipulate Locke to reach his loophole.
I don't really know if thats a theory or if its just summation of facts or if everyone got that already but its what I got.