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(Nothing in here is a spoiler. It's my theory and if any bit turns out to be true it is coincidental and not from previous knowledge.)
I think I've figured out the loophole that let Ben kill Jacob. What it is, I think, is wanting to kill Jacob. Actually wanting to in his heart, which for the purpose of this theory means having a legitimate reason to hate Jacob and want him dead. It seems too easy, but here is my reasoning put into numbered points for no reason:
1) When the Man in Black told Richard to kill Jacob, it seemed as though Jacob didn't know that's what the MiB is up to, despite MiB warning him that he'll find a loophole someday. Jacob also seemed genuinely stupefied when Richard told him the MiB will interfere with people even if Jacob won't (how long have these two been on the Island, and how many people have they brought again?).
2) They both know the basic rules, and those include that they can't kill each other but can be killed by others. Jacob jiujitsu'd Richard because the MiB isn't following the rules. Richard didn't want to kill Jacob in his heart. He was just doing it for ulterior motives (lies and false promises of getting Isabella back).
3) The MiB genuinely thought Richard could pull it off as long as Jacob didn't have a chance to convince him otherwise. He though he convinced him enough so that Richard really wanted to kill Jacob. This is why MiB told Richard his offer always stands, because Richard could then actually kill Jacob legitimately. He just didn't have a reason to want to kill Jacob deep down at the moment.
4) The MiB makes a plan to have Ben kill Jacob because he knows Ben feels betrayed. Ben works for Jacob and even though he hasn't met him he still knows basically what's going on. He legitimately, though still somewhat manipulated, in his heart wanted to kill Jacob. This is because Ben is a self-centered prick and thinks Jacob is being unfair.
5) Jacob's last and only defense was to tell him he had a choice. Ben made the choice to kill him legitimately at this point. After his talk with Richard, had Richard really wanted to still kill him he could have. Jacob is allowed to tell truths and not manipulate, and that's all it took to convince Richard he's the good guy.
6) When Richard called out for the MiB before Hurley arrived, the MiB didn't respond because Jacob is dead and Richard is useless. MiB really was going to kill him or at least keep him away from his enemies by taking him on his side, but Richard's rejecting him earlier changed his mind. Or he was just too far away and Hurley got there first.
7) The thing with Dogen having Sayid kill MiB could work on the same premise. Sayid didn't trust Dogen but attempted to kill the MiB. The MiB just took the stabbing because he could sense that he didn't really want to kill him. The smoke monster is known to be able to read minds, plus the illness he has might link him to the MiB. Either way, he wasn't worried about being killed. Instead of telling the truth, he then manipulated him to be on his side. He had to lie because if he told Sayid the truth, he could and probably would decide to kill him, deep down in his heart.
8) Essentially, Dogen made the same mistake as the MiB. Sorta. He told Sayid the truth about the MiB being pure evil and that he could end him and prove his goodness, but Sayid didn't believe it. Contrast this with MiB straight out lying to Richard about Jacob having Isabella. Either way, neither Richard nor Sayid wanted to kill Jacob or MiB in their hearts.
9) The task Jacob is preparing Jack for is killing the MiB. Jack has to come to the decision on his own and want to do it in his heart. He can't do it if he takes over for Jacob, so someone else (Kate?) will have to do that, or there won't have to be a new Jacob at all if MiB is dead. Jacob won't lay it out for Jack because he wants to prove people will do the right thing without him intervening. It's also possible Jack's task really is to take over for Jacob and someone else, hopefully Ben for the sweetest bit of irony in television history, will kill MiB.
Please comment! I want to hear what you think, whether you agree or not and what your reasons are.