"Evil" may be a bit strong. But it sounded good for a title, so be it.
First, some methodological considerations. Clearly, this will be a critical analysis (I found the series, including the final episode to be very entertaining, but also evil), and doing such, especially early, always has its dangers. But, it is a TV show, so I'll take the associated risks. Second, the show has a plethora of unsolved mysteries. There are many reasons to leave mysteries unsolved (inability to solve them while remaining entertaining; they were meant to be left to the viewer's imagination; they were merely devices to move the plot; etc.). Yet, in spite of these various possibilities, I take it that a theory that explains more mysteries is to be preferred, all things considered, to one that explains fewer. Third, though I have done a bit of research before writing this, I surely have done less than I could have. Finally, I state the obvious in certain places precisely because there seems to be confusions over the obvious when it comes to LOST.
Christian Shephard nearly-clearly explains much of the show's meaning at the end. The Island was real, everything that happened on it was real, and everyone on it was real. The side-verse (the alternate timeline we received throughout the final season) was not real. It was purgatory. And, the show ends with them heading to Heaven. This we all know pretty much for sure.
Now, there's two possible stances we can take on this Heaven ending (which is reminiscent of BSG): either it was a deux ex machina used to wrap everything up in a Pollyanna sort of way to make everyone happy (while at the same time allowing them to come off as a serious show that was willing to kill off major characters who no one wanted to see die), or it was planned all along and fits with the major themes of the show.
I think it is too easy to conclude the former; the latter is in fact correct.
So, here's the less important bit: the true meaning of the central plot element. The energy source in the middle of the island is not merely a MacGuffin. It is the energy source that powers the path from Earth to Heaven (or just Heaven -- I believe it is the former, but I'll discuss it as the latter for sake of ease). I'm fairly confident about this.
So, why think it? Because all signs point to the idea that extinguishing the energy source would lead to unspeakable evil being unleashed throughout the world. But this doesn't yet make sense. Suppose we let the energy source that powers Heaven die out. Why would that unleash evil? Wouldn't the power source for Hell make more sense here?
You would think so, but that would be to miss the two more important bits: the show is in the end, and always has been, about free will and faith. I might be wrong about the power source for Heaven bit, but I'm not wrong about the free will and faith bits (and I conclude this about both, even though only free will seems to be openly discussed amongst the makers of the show).
The latter two help explain the Heaven part. The reason we can see that the source powers Heaven is because (a) the Island is clearly intended to be a positive thing; and (b) it fits with the narrative that it is nearly impossible for humans to freely choose goodness unless they have faith in their salvation. Thus, were the energy source for Heaven to be squelched, there would be no salvation, no faith, and no goodness (so the show writers would want us to believe).
Thus, Jacob's tests are explained (Jacob is the Man in White, who it turns out was once just a regular boy, but who became the protector of the island, which led to superpowers of sorts and a lifespan that lasts several hundred years at least), as are the constant failures. The entire point of Jacob's tests is to discover a person (or group) that was morally pure. But, this moral purity is not one of doing good acts purely for the sake of goodness. No, it clearly is a purity that is found in belief in a higher power without question or reasoning. Jacob required blind faith all along.
This point is a reoccurring theme throughout the show, even long before we meet Jacob. But certainly in his every episode as well. The Man in Black (MiB) actually was quite reasonable (though it turned out he was lying): he provided explanations for his views, and reasoned with each candidate for why they should join him in what seems like a perfectly sane task that all could agree with -- leaving the Island.
Jacob on the other hand consistently (merely) insisted that others do as he told them to. Even as Ben is about to kill him, he merely tells Ben not to. But MiB actually reasons with Ben, and provides further evidence, such as in his appearance as Ben's daughter. MiB represents (here and elsewhere through the show) reasoned and evidenced based modes of persuasion. Jacob represents blind faith. Sure, MiB is lying. And sure, that's clearly important. But, how can anyone know that? Well, like in every previous season, they can only know by relying on their deep feelings and instincts (such as when Ben, in every previous season made demands that ran contrary to demands made by ghosts, the real Locke, and others who likewise provided neither reasons nor evidence).
And, in fact, the characters who turn out to be right, amongst the candidates, are the ones who allow themselves to be guided only by their instincts: Locke and Hurley are right about the Island and their views from the beginning -- though it is not at all clear why they should be (they never had evidence for their optimism and reliance on the Island's magic). The characters whose thinking is more reason and science based (Jack and Sawyer) turn out to be completely wrong -- until the very moment when Jack finally comes around and lets go... of SCIENCE and REASONING. And then it is Sawyer who refuses to merely trust Jack and gets Jin and Sun killed.
Thus, one cannot fully understand the show by concentrating on free will alone. Free will makes the most intuitive sense when it is coupled by options -- and those options are made most concrete when at least one is made substantial through the representation of a correct path. In this show, what makes the options concrete is faith, as backed by intuition. One chooses well when one chooses to believe blindly in those who one intuits are good.
Sawyer should have listened to Jack.
Jack finally listened to Jacob.
Locke and Hurley listened to the Island all along.
Everyone who listened to MiB's reasoning, and acted based on his provided evidence, failed. Just as Michael ended up killing Ana Lucia and Libby, simply because he believed the wrong people (and he, therefore, is undeserving of salvation in Heaven, and must forever suffer -- though Sayid the torturer is allowed in). They chose their reason over blind faith and intuition -- and they paid the price.
Thus, it turns out that the right decision was to save the energy source. Why? None of the characters are ever told -- they cannot be. The mysteries cannot be solved for them; if they were solved, they wouldn't be believing on blind faith alone. They are merely told enough to be able to obey. If they don't obey, they lose Heaven for everyone. And with the loss of Heaven, we would all lose faith, and we would necessarily turn to evil. But, in the end, even the man of "science" turns over to faith, and the Island is saved. Thus, they can all go to Heaven.
So, why does God put the energy source for Heaven in an Island on Earth? Because humans as a whole wouldn't deserve Heaven if none of them were able to protect it based on their faith in those who are giving them orders to do so, without any basis in reason or evidence.
The Island is the test that proves our worthiness of Heaven -- and Heaven is the precondition of our ability to be good. Thus, all goodness derives from a gift that we earn by ignoring our rationality.
So, in the end, I think the show was evil. Well, maybe "evil" is too strong, like I said. But, this entire idea -- that pure morality is based on ignoring reason and going with your faith, which tells you to follow orders from people that you intuit are good -- is clearly a good source of evil. It is, in fact, a necessary ingredient for all the great evils in the history of our race, give or take a massacre here and there. So, in supporting this premise throughout the show, I suppose that does in fact make the show evil.