This theory is building upon "The Knife Theory", which was good stuff. I find it extremely difficult to stick to one topic when writing these theories, so I will try my best...
First of all I want to point out that I believe Richard and Jacob to be "the bad guys". LOST is a show where nothing is usually what it seems, and most characters are usually not who they appear to be initially. For example, we were lead to believe that Jack was going to get everyone saved, when after all was said and done, he ended up killing everyone aside from those who got off of the island and the Sawyer/Faraday crew. We were lead to believe that Sawyer was a bad guy the first few seasons, only to see him turn out to be one of LOST's biggest heroes. Ben Linus and Juliet both come across quite evil in season 3 but end up helping the survivors later on (Ben is the only character on LOST where I have no idea still if he's good or bad).
Anyways, my point is, things are usually never what they seem on this show, especially with the characters. We've seem very little of Richard and Jacob, but they have both come across as very "good" characters. But think. Jacob allows Kate to keep stealing. He ENCOURAGES Sawyer to kill Cooper basically. He pulls Sayid out of the harm's way when he KNEW Nadya would be killed, and he let her die. Richard on the other hand is extremely mysterious. We've seen him kill several people without hesitation, poison the entire Dharma Initiative to death, and we KNOW he is the only character besides maybe Ben, Eloise and Widmore to have been inside the Temple AND to have direct communication with Jacob, meaning that there's a LOT we have been kept in the dark about thus far with both Richard and Jacob. Just because they come across as mostly "good", they have both done some terrible things, just as bad as any of the other characters on the show.
How does this tie into the Knife Theory?
Richard, presumably after seeing "future Locke" in 1954, visits young Locke and sees a picture on his wall of the smoke monster killing someone, and is seemingly happy about it. He then tells John to pick the item that it his (being the "Leader" of the Others and Jacob's protege as he told Richard in 1954, he should have chosen the Book of Laws, which seemingly is the set of rules that the Island follows or whatever), but Locke picked his knife and Richard was PISSED. Richard is rarely pissed. Why did Locke pick the knife? Why did Locke draw the picture of the monster and why was Richard happy about that?
Let's go back to John's life story for a second. We all know the tragedies he's suffered, we all know that he never felt like he belonged anywhere until he landed on the Island and seemingly transformed overnight into a knife-throwing, expert-tracking, badass hunter who could kick anyone's ass. We all know that Anthony Cooper is not Locke's father too.
Locke had never been happy at any point in his life and deep down, he knew that he belonged somewhere else that he could never seem to find. Where should he have been the entire time? The island. I'm not going to get too into the time travel, alternative reality or body snatching stuff, but it's pretty clear that Locke belonged here the whole time, and he knew that as soon as he woke up and could move his legs. In season 3, we flash back to Locke on the marijuana farm, and the kid tells Locke he won't shoot him because he's a good man, while Locke insists he is a hunter, not a farmer. In "Walkabout", everyone keeps trying to tell Locke he can't be a hunter and he can't do this and that, and Locke angrily says "DONT TELL ME WHAT I CANT DO!" After Locke wakes up from the Hatch explosion and rescues Eko, Eko says "You are a hunter, John". Eko is killed the next day by the smoke monster, who seemingly did not want Eko to continue to influence John. Perhaps the monster had been t! rying to stray John away from his destined path so that Jacob would not eventually be killed, and wanted Locke to lose faith. Perhaps that was the Monster's goal from the beginning - to break John's spirit and turn him back into a whimp so that he would never go through with killing Jacob.
The REASON I think Alpert was angry that Locke picked the knife, was because as we've seen, Alpert (along with Ben, Widmore, Eloise, Abbaddon, maybe Jacob, maybe Faraday, etc.) KNOWS THE FUTURE. They KNOW whats going to happen, and some of them are working hard to prevent it, while some are trying to do anything they can to make sure it happens. Richard was pissed because he knew that Locke was always meant to be a warrior/hunter, and he knew that he would one day kill Jacob if he picked the knife, so after he does, Richard and CO. attempt to make Locke's life a living hell so that he'll lose faith and become a whimpy old man, which they succeed in doing - until he gets on 815 and lands on the island, where someone or something wants to give him his faith back and make sure he becomes a hunter and eventually kills Jacob (MIB?).
I think Richard has been manipulating Locke from the beginning, but its too hard to figure out exactly how and why. I don't know where Ben comes into play in this, but he clearly is involved. My point here is that Locke becomes a warrior with his knife when he gets to the island, loses his faith in season 2, gets back on the path in season 3, and continues towards the eventual death of Jacob. Richard knew that by Locke picking the knife, that this is what would happen, which is why he was so angry. Locke's destiny WAS always to kill (evil) Jacob - And as soon as Richard found this out, he made every attempt to stop Locke from becoming who he was destined to be which is why Locke never felt "quite right". Maybe Richard/etc. hired Cooper. Maybe they arranged for Emily Locke to be hit by a car and give birth to John 3 months early. Maybe they set John up to fail throughout his whole life in hopes that he wouldn't become who he was destined to be and kill Jacob. I think Abbadon ! might be one of the good guys, who wanted to make sure that Locke ended up killing Jacob. Who knows - maybe even Widmore is one of the "good guys".