That appears to be the same reason why Jacob kept people like Ben and Charles and co. around (I would also not be too surprised if it turns out he is also trying to find a way to free his brother's soul down the line, even if it meant finding someone to give to Smokey in his place)

It seems the Guardian not only has to find a suitable candidate to take his place, he also needs to find someone who can kill him.

Mother had found her two in the twins. I think she destroyed the well to make sure MIB couldn't leave the island, and to piss him off so he killed her. Right after she destroyed his stuff, she made Jacob her heir. She knew.

Incidentally, it probably wasn't Jacob's intent at all to get killed by Ben before a new guardian was picked. That seems to be MIB's plan to prevent Jacob from creating a new guardian. With Jacob out of the way and having taken the body of one of the remaining candidates (and Jack's opponent, to boot)and controlling Jack's sister he could use as a mole/weapon, MIB thought it was only a matter of time before he managed to divide the candidates and made them kill one another.

I think this is why Jacob's soul is still bound to the Island, while mother's seems to have been freed. I think Jacob won't be freed until/unless a new guardian is made. This must be why MIB is disturbed by Jacob-as-a-kid appearing. He didn't expect that, he thought he'd be rid of Jacob just like he was rid of mother after killing her.