not literally Sobek and Anubis, but interpreted as such

http://www.imdb.com/title/tt0411008/board/flat/155631338

Jacob has for centuries lived under a giant statue of (most likely) Sobek (the Egyptian crocodile deity), and in the tunnels under the temple where the smoke monster appears to dwell (at least sometimes), there is a carving of Anubis (the Jackal deity) facing an abstract creature that vaguely resembles the smoke monster.

So, in some sense, it would seem that there is some correspondence or connection between Sobek and Jacob, and between Anubis and Blackshirt (Jacob's nemesis).

My point here is that Jacob and Blackshirt don't need to literally be Sobek and Anubis, but rather that they are similar enough to them, that they were identified as Sobek and Anubis by previous inhabitants of the Island, who had an Egyptian cultural background.

That is, it seems highly likely that at some point some Egyptians inhabited the Island, and built the various clearly Egyptian-looking things on the Island, e.g. the Sobek statue, the tunnels under the temple, etc.

How did they get there? Don't know. Maybe they were Egyptian sailors who ventured far and wide. Maybe (since the Island moves) it was at one point relatively close to Egypt, e.g. somewhere in the north-western Indian Ocean.

What happened to them? Perhaps they killed each other, and died out. When Blackshirt is describing groups of humans who have come to the Island in the past only to "fight, destroy, corrupt". the Egyptians are just one of many examples of this, perhaps not even the first.

Anyway, the Sobek-Jacob and Anubis-Blackshirt connections are attractive. I know relatively little about Egyptian mythology, but Anubis is a judge of the dead. Anubis weighed the heart of the dead person against an ostrich feather, and if the heart was heavier (due to its burden of sin), the dead person is devoured by the monster Ammut. Thus, Egyptian people on the Island could have interpreted Blackshirt as Anubis, and the Smoke Monster as Ammut. It does look like Blackshirt and the Smoke Monster are most likely one and the same, in which case he is both judge and executioner, but even if not, they are very closely linked. I know even less about Sobek, but there are references online to his having the ability to undo evil, or transform it into good. Thus, Blackshirt simply wants to judge and devour the wicked mortals, but Jacob wants to reshape their evil into good, and their disagreement might be over whether this is possible.

...

I don't know what the loophole is. Maybe Blackshirt can't kill Jacob directly, but he can convince someone else to do it. That seems a little weak, but anything beyond Blackshirt not being able to kill Jacob has to be pretty speculative. For example, maybe it helps that Ben was at one point anointed as the leader of Jacob's people, or maybe it helps that he turned the wheel... I really don't know.

In any case, I personally think that although Jacob is dead (at Ben's hand), he saw this death coming from a long way away, and has been preparing for it. Note that he makes no effort to dodge Ben's knife, or even to persuade Ben not to do it, beyond simply informing him that he has a choice, i.e. free will. Jacob's last words, "They're coming" probably refer to the people who he touched in the flashback scenes, i.e. Kate, James, Jack, Hugo, Jin, Sun, Sayid, Locke, and possibly Ilana. Why is he physically touching them? Perhaps he is transferring some elements of his powers to them, in pieces, for some purpose that has not yet been revealed. Perhaps the incident will warp Kate, James, Jack, Hugo, and Jin back to the present, to join with Sun and Ilana to confront Blackshirt, and to eventually counteract the 'change' that he promises to Ben. Jacob told Blackshirt that when Blackshirt found his loophole, Jacob would be right there, waiting for him. I interpret this not as an idle 'bring it on' type comment, but as a correct prediction of the future, which implies that he has no intention of trying to stop Blackshirt, but that instead he will in the meantime work on some way to plan beyond his own death, and to turn even that evil into good...

There are a lot of different people who have come to the Island independently, e.g. Richard's tribe of Others, the Oceanic survivors, the Ajira survivors, Widmore's get-Ben expedition, Desmond, Rousseau's team, the Black Rock, the Egyptians, the Dharma Initiative, the Nigerian plane, and probably many others. Did Jacob 'call' them all to the Island, in whatever way Blackshirt is suggesting that he brought the Black Rock? It's quite possible.

The Others or Hostiles are a group with unknown origins, but which probably began after Jacob and Blackshirt's conversation (which may imply that there are currently no mortal people on the Island), perhaps with the Black Rock. Richard has been part of that group for a long time, again, perhaps since the Black Rock. At some point, he was given agelessness by Jacob. The tribe seems to pick up other people along the way through a variety of circumstances, e.g. Widmore, Hawking, Ben, Juliet, etc. In the 1950's, the tribe kills a group of US soldiers in possession of an H bomb. In the 1970's, they feud with the Dharma Initiative and are called the Hostiles. Eventually (in the 90's?) they kill most of the DI, and take their barracks and many of their research stations. In the 2000's, they feud with the Oceanic survivors and are called the Others. In the present, they are apparently divided into two groups, one with Richard and fake Locke at the Sobek statue, and one in the temple.

I doubt that Blackshirt is really 'sympathetic' to any mortal human beings; he finds them to be weak and corrupt by nature. He shows no sign of caring about anyone at all; he simply uses people as pawns toward his goal of killing Jacob. Exactly why he wants to do this is still something of a mystery, but it might have something to do with Jacob keeping his powers in check, saving people whom he wants to condemn and devour, or something like that.