DarthYam, as we talked over, I will now put my theory on this. Due to the contradiction and retcon problems between SC1 and SC2's lore, I'll try to tie them together as best I can.
In the beginning, when Amon decided to make a master race via the hybrids, it was for the sake of mixing the Zerg and Protoss together. His uplifting actions on Aiur are proof of this, but as Rohana had pointed out, the Firstborn grew beyond his control. Despite being forced to leave Aiur, Amon still considered his actions with the Protoss a success in the future. By around 500 BC, when Khas rediscovered the Khala link in the Xel'Naga Caverns, thus marking an end to the Aeon of Strife, Amon and his followers were still at Zerus, where they were confronted by the regular Xel'Naga. Despite his work not being finished on the Zerg, he unleashed the swarm to kill them off. Amon himself was defeated however, and forced back into the Void, where he remained for the next 3000 years until the events of SC2 finally set him free again.
Many had asked: why was Ouros allowed to live? If Amon was going to be "revived" anyway, why didn't Duran just kill Kerrigan to ensure the key to stopping him would be lost?
My theory on that is the following:
The regular Xel'Naga knew all along that destroying Amon's physical body would not kill him, but merely force him back into the Void. They knew that being forced back there meant nothing, as Amon could just return to the material universe. Therefore, when Amon was forced back into the Void, they decided to imprison him in a place where the Void energies would slowly kill him. Amon had Ouros captured in the hopes to drain his essence in order to break out of that prison, but Ouros and the regular Xel'Naga already thought of that, and ensured that the prison Amon was put in was a place he couldn't escape merely by draining the essence of other Xel'Naga.
The result of this was that Amon decided to do the next best thing: draining Ouros's essence as a source of life energy. It won't set him free from the prison, but it would keep him alive. However, Amon and Duran both knew this was only a temporary solution, since Ouros's essence could not last forever. This would be consistent with what he said to Kerrigan in "The Essence of Eternity" mission of "May the last of my essence give you the power you need."
If so, then it means by the time of SC1, the situation had gotten desperate. Recall back in HotS where Kerrigan and Stukov were discussing about the hybrid. Kerrigan theorized that the hybrid collect psionic energy, and Duran must use that psionic energy to help his master. The war between the Zerg and the Protoss was to do just that, as the psionic energy released from the war would be collected by the hybrids, and eventually Duran would stockpile enough to have what he needs. Both concluded that when Raynor blasted her with the artifact at the end of WoL to deinfest her, Duran used the psionic energy she possessed and transferred it to Amon. This would then be consistent with what Duran was telling Zeratul in "Dark Origins," that Kerrigan's integration to the swarm had sped up his progress.
In reality however, it wasn't about speeding up the progress at all. Rather, it was a race against the clock. Likely what happened was that after 3000 years of draining Ouros's essence, the amount still left in Ouros was no longer sufficient to keep Amon alive much longer. However, he was still stuck in the prison that the Xel'Naga put him in, with no way to break out without sufficient psionic energy. To make matters worse, the war between the Zerg and the Protoss hasn't been in full swing for very long. Remember, according to the SC1 lore, the swarm set course for the Koprulu Sector in 2439, and although there was some encounters with the Protoss along the way, it was relatively rare between the years 2439 and 2499.
The dilemma facing Duran, therefore, was simple: the psionic energy he needed to help his master simply wasn't pouring in fast enough. Therefore, Duran must have realized that at such a rate, it would take decades (or even longer) before he would have enough stockpiled psionic energy necessary to free Amon, and by then it'll be too late for his master because Ouros's essence was mostly gone, and the prison Amon was stuck in would kill him. Clearly, in Duran's eyes, a different strategy was needed.
That would then explain why Duran let Kerrigan live despite the possible threat she could pose: he needed her psionic strength to grow in the years after BW so that once her power was drained, Amon would still be alive, and have what he needed to free himself from the prison.
But others may argue: if Amon needed the psionic energy to pour in faster, why the hell didn't he just tell the Overmind the location of Aiur? An attack on the Protoss homeworld would certainly have caused plenty of psionic energy to be released, and surely that would have helped him greatly.
Here's a possible theory: When Amon created the Overmind, he created it so that the Overmind would only respond to his commands. The Overmind would not respond or listen to anyone else, not even his followers, including Duran. Failing that, perhaps he did plan for the Overmind to listen to his followers, but he hadn't gotten to that point yet.
The bottom line is this: when the regular Xel'Naga confronted him and his followers at Zerus, the Overmind at that point in time had only been designed to obey his orders, and no one else's. Furthermore, at that point in time, because his work on the Zerg wasn't yet finished, Amon hadn't told the Overmind the location of Aiur. As a result, when he was forced back into the Void, the communications link he had with the Overmind got severed, and the Overmind never knew anything more than just a vague idea of where Aiur might be. This would then be consistent with the events of SC1, and why only after Zeratul killed Zasz did the Overmind finally discover the exact location of Aiur.
The problem facing Duran, however, was that he couldn't have known that. After all, the coming to Char wasn't the Protoss did simply for the hell of it. It was due to Kerrigan's psionic enmanations from within the chrysalis that had drawn Tassadar and Zeratul to Char, as explained in the events of SC1. When they first arrived on the the planet, they didn't even know this was the base of operations for the swarm within the Korpulu Sector. Furthermore, since Khala energies were useless against Cerebrates (as shown in SC1 ep3), 'killing' a Cerebrate in such a way would not have allowed any Protoss mind to touch that with the Overmind's. The bottom line was that had Zeratul not been drawn to Char, Zasz would not have been killed, and the Overmind wouldn't have known the location of Aiur.
Thus the problem Duran faced by the time of SC1 was the following: how could he have known Kerrigan was even going to get infested in the first place? And therefore, how could he have known about Zeratul being drawn to Char, the killing of Zasz, and the mind touch with the Overmind which would have finally allowed the swarm to locate Aiur?
To me, it seems like during those 3000 years between when Amon was imprisoned within the Void and when the events of SC1 happened, Duran would have needed to proceed under the assumption that the Overmind was not going to be able to locate Aiur in time in order to take the fight to the Protoss in order for him to get enough psionic energy stockpiled in order to help Amon.
Therefore, we must look at the quote Duran said in the "Into the Void" mission of "The swarm had one purpose: the assimilate the Protoss and create the hybrid. Now you are no longer needed." This sentence is true, but Duran failed to mention is the timing factor. If the hybrids could not be created quickly enough, then it'll all be for nothing because the prison Amon was stuck in would kill him.
Let us now go back to "Dark Origins," along with what we know from LotV: it would seem that once the 2nd Overmind was killed and control of the swarm lost to Kerrigan, Duran simply switched production methods: instead of using the swarm to assimilate the Protoss to create hybrids, he decided instead to use terran tech to breed them instead. We saw that back in "Dark Origins," and this was further explained upon in "Templar's Charge," where Karax confirmed that it was via the Moebius production facility at Revascar that Amon's hybrid armies are born.
But once again, the timing plays a critical factor. After all, how could have Duran predicted exactly when the Overmind would finally know the location of Aiur? For all he knew, it could have been thousands of years after the events of SC1 and SC2 before the Overmind finally found out, and by then Amon would have been long dead. Do not forget, the psionic energy to release Amon from his prison could not have come from the swarm itself, since according to the SC1 manual, the Zerg themselves didn't have too much psionic powers (prior to Kerrigan becoming part of the swarm).
Therefore, it would have been vital to take the psionic energies of another species in order to help Amon. Since the terran race was still in its infancy (this is true even by the time of LotV as the average terran had no psionic abilities at all), Duran knew it would have been vital to take the psionic energies from the Protoss instead. But if the Overmind could not locate Aiur quickly enough, then Duran would have deemed it necessary to find another way drain the Firstborn's psionics.
If that's true, it would only make sense that Duran would have begun the hybrid production via terran tech (or any non-Zerg assimilation method) long before the events of SC1 happened. It would be the only way to help his master, after all...