I can name hundreds of characters who do evil in the name of good. For a powerful literary example I'll point to a section of Robert Jordan's wheel of time, now this takes place in the latest book, finished after his death by another author but I've read it and it's still an amazing book.

A man is captured by one of the most powerful power users of the age, she is one of the most dangerous, not just because of her power but because she likes to compel people innocent people to do her bidding. She compells a messenger to go to the Dragon Reborn, Rand Al' Thor and invites him to her palace. Rand cottons on to the man's condition in part because inside his head he hears the thoughts and voice of "the Dragon" Lews Therin Telamon. Rand forces Nynaeve a close friend and perhaps the most powerful woman alive in terms of raw strength and healing capabilities to remove the compulsion so he might learn the location of the forsaken one, doing so killed the man. He did however get the information he sought and then to make sure he utilized a lord of the nation he was in to send a message replying to the forsaken to her palace alone and unarmed. The lord returns heavily compelled to invite Rand to go with him to her palace. At that point Rand draws as much of the power as he can and forms a weave of power so destructive it's forbidden never used by friend or foe. In fact it had been forgotten (mainly due to the forsaken being bound for thousands of years behind cuendillar seals) for thousands of years until the thoughts of "Lews Therin" made Rand perform the weave in a battle against the forsaken and worse. Balefire will not only destroy and kill but will physically erase the things it destroyed, it is as if they never were, depending on the size of the balefire beam and it's power the more of the history of the victim you erase, things they do are undone ect ect. He doesn't go in to the palace which he knows is a trap regardless of the hundreds perhaps thousands of people there, he burns it from the pattern with balefire. How does he justify killing so many people? "Her abilities lie in playing games, when you know you're out smarted you make them believe you're going to sit down and play their game then when they start to think you will, when they don't expect it you reach out and punch them as hard as you can in the face."

The Dragon Reborn or Rand Al' Thor is such a good example of this because he is destined from before he was born to fight the dark one, the worlds equivalent of the devil a source of pure evil. He is all that symbolizes good and justice in the world he must break down the nations and unite them to form an army capable of taking the fight to the enemy. He is also destined to go mad, he must use Sadin the male half of the one power to defeat foes what he cannot best with sword alone and in doing so he will expose himself to a taint placed upon Sadin by the Dark One when he first fought the original Dragon, Lews Therin in ages past. Because for longer than living memory all male channellers have gone mad and died horribly or been caught and executed for the crime of being a man who can channel there is no one alive who can teach him except for his greatest enemies, the forsaken. Rand does end up imprisoning the weakest of the Forsaken for a while to learn from. He also learns from the memory of Lews Therin in his head. The thing that makes Rand so chilling at times is not the madness he has from having wielded tainted power for some time (even though he cleanses it eventually) it's not even the imprisoning his enemies so that he might learn it's the sane, rational decisions he makes such as the way he defeated the forsaken in the above passage. He literally was prepared to calmly, cooly destroy as many innocents as he had to without thought for them purely to kill one woman.

In movies/tv I would point out the recent series Chris Ryan's strikeback. In that a british soldier (Collinson) attached to an SAS squad for a rescue mission makes a mistake, he hears boots on a stairway and opens fire he kills 2 of the SAS squad as they come up the stairs and mortally cripples a 3rd because bullet fragments become embedded in the soldier's brain. He has an opportunity to come clean and he out of fear for himself covers it up. Instead the commander of the squad (Porter) takes the blame, he is pensioned out of the regiment and his wife and daughter leave him because everyone assumes including him that he is somehow responsible for the deaths of his 3 best mates. Meanwhile the actual killer escapes recrimination, he becomes a decorated soldier, a war hero who later ends up heading up a British intelligence division tasked with running missions such as the one he was on originally with (Porter) the SAS. He ends up using Porter as an agent to rescue a hostage reporter in Iraq because Porter believes he has seen the only lead they have before, as a child rigged to be a bomb out in Iraq when the original mission to Iraq to free a hostage took place. Porter should have executed the boy but he instead knocks the boy out. Out in Iraq Porter gets himself captured by the terrorists and before he and the reporter get executed he manages to convince the boy now a man to help him escape. They make it to the rendezvous with the chopper when Porter and the reporter get aboard the chopper the command comes down from Major Collinson that the boy is not to be allowed on the chopper even though it's a complete death sentence since the terrorists are literally 30m away shooting at them.

Collinson does good in the fact that he is rescuing people and defending his country (if not in person in the field he still gives the orders what allow this to happen) and he genuinely does support Porter in the field even though if Porter does find out the truth his career is over. However he commits acts of evil such as forbidding the extraction of the terrorist who helps Porter escape (Asif) because if Asif were to speak to others he could reveal the truth of who killed the 2 british SAS troops and crippling a third. He commits acts of evil to protect himself and his position but his position allows acts of good to occur.