Although I agree that good vs. bad is one of the theames of the show, I do not know if it is good vs. evil. This goes along with the Black/White, references of the show. It is all about balance. Black balances out white, good balances out bad/evil.
As for Charlie being evil and becoming an other, we know that will not happen. Ethan hung Charlie from a tree, and thought he killed him. Only Jack and Kate saved him from that fate. If the others wanted him, he would have been taken then, but they took claire, the only one they wanted, and they only wanted her for the child, not her. As Alex told us, when she freed Claire, she said their going to take your baby, and you will die or something.
Also remember the list, Godwin or whatever his name had. It only had the Good People on it. They left the non-good people off the list. We also know from Zeke that he was mad at Ethan for not getting the List for the other group (main group). So we do not know which others from the main group are wanted by the others.
I don't see the others needing protection from anything either. Zeke said, you are on MY ISLAND. And you are here only because we let you be here. That does not sound like people who need protection from anything. I think they control the island/experiment. They have a boat, medical supplies and equipment, medicines, food, power, the ability to move as they please, etc etc.
All this speaks to is Motive. Do we know they are evil, or good. We will never know that until we know their motives for wanting children, and certain other people.
Also, as the spoilers point out that we will soon know why the plane crashed, I am going on the assumption that the others are reponsible for bringing them to the island. Agian this points to them being in control on the island. So what do they need protection from?
As for Desmond, Desmond wrecked on the island and was taken to the hatch by Kelvin. Together, they continued the protocol set in place by Dharma since THE INCIDENT. The protocol consists of them taking shifts and entering the numbers into a computer every 108 minutes. Eventually, Kelvin died, and Desmond was left alone to do the work himself.
There is no mention or inkling that Desmond had contact with the others or even knew about the others. Kelvin could have been unaware of them as well, as he was told not to leave the bunker. He would have thought he was to hit the button, take his meds, and not leave the safety of the hatch as he would get exposed to the sickness. Then he dies? Would the others not have replaced him if they were in contact with the hatch folks? Who knows.
As to finding Desmond with the others? That is a possiblility. I do not think that Michael will be with them though.
Also, Danielle says that the monster is a security system. And goes on to say its purpose is that of any security system. That being to keep people/things out of an area and alert the operators of a security system when the area being watched is breeched. This also implies that they control the monster.
All that being said, until we know what the incident was, we will not know if it is just another ploy to work on the minds of the hatch button hitters and keep them in line, or if it truly represents a loss of control incident over the experiment that was being conducted.
So I think Good vs. Evil does have a component to the mystery of Lost, but I think what is acutally going on goes much much much deeper.
Food for thought.
It is astonishing how foolish humans can be in groups, especially when they follow their leaders without question - States: The Bene Gesserit View. All States Are an Abstraction.