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Star Wars Force Commander: After proving their loyalty in combat, Tyr Taskeen allows several imperials to join the Rebellion as trusted officers. This is common in the Star Wars universe; defectors are only executed if discovered before they actually defect. Their new superiors trust them after a heroic action or the revealing of top-secret information. 
Tomb Raider (2013): When Whitman betrays Lara and co. by handing Sam back over to Big Bad Mathias, the latter rewards him by tricking him into approaching Himiko's Stormguard as a distraction and then slipping by with Sam while he's being torn apart.
In Warhammer 40,000: Dawn of War: Dark Crusade, during the Imperial Guard stronghold assault, the Guard's Fifth Company can be turned rogue and allied to the attackers' faction by killing their Commissar. After the battle, if you were playing as the Space Marines, you see the Marines sending the survivors back to Segmentum Command, with a request to their superiors to not punish the Guardsmen because they followed their orders and fought with honor... except Fifth Company, who the Marines summarily execute for treason. Ironic, isn't it?
Also occurs in vanilla Dawn of War's campaign. Said traitor (Isiador) steals the MacGuffin from right under the other space marines' noses, only to have the Big Bad immediately take the item for himself and leave the traitor and his marines to guard the rear. Meaning he has to face the very angry Force Commander/former best friend he had just betrayed. Needless to say, he doesn't last long.
The Operation Flashpoint expansion, Resistance, has an alternate ending (though it occurs after the 3rd mission) where you betray the Resistance to the Russians. Immediately afterwards, you and the remaining Resistance members who have been captured are taken to the General, who orders the prisoners execution. As they are being lined up, a officer asks about your character — he orders that you be executed as well, because you are seen as 100% untrustworthy.
In Fire Emblem: Path of Radiance, the half-cowardly, half-Apathetic Citizens of a port town inform the Daein soldiers about which boat Ike and his company took. When they ask for their reward, they are told that it was their country's own princess in that company that they just sold out. Just as the realization and guilt really begin to sink in, the captain of the soldiers has the "dastards" taken away to be worked to the bone, a "fitting reward" for people who would sell out their own princess.
In Fire Emblem Awakening, a man who Chrom knew well sold out Emmeryn (his sister) to the Plegians. He's slaughtered at the spot of the ambush.
In Prince of Persia: The Sands of Time, the Prince regrets that his father did not give the Vizier this treatment, as he betrays them almost immediately after betraying his former liege and joining them.
From the Point Lookout DLC, a question from a Brain in a Jar: What is the greatest thing man can acquire? Answer 1: Something that I'll give to you if you backstab your ghoul partner. Answer 2: Death. Said brain betrayed the ghoul back when they were still human, so genre savvy players will recognize that one insane (read: lobotomized) vault dweller versus a brain in a jar and a small army of robots with frickin lazer beams is very less likely to win than one insane vault dweller and one experienced robot scientist versus a brain in a jar and a small army of robots with frickin lazer beams. Hence the backstabbing.
Also occurs in Fallout: New Vegas, though not with you. Caesar's Legion was offered a deal by the town of Nipton: in exchange for a sum of caps, the mayor would round up NCR troops and Powder Gangers inside the town and trap them. The Legion captures everyone - including those who were helping - and plays a game with them. It helps that Nipton was a Wretched Hive and the mayor was an unscrupulous jerk, though most people consider this their Moral Event Horizon, given the brutality of the Legion.
At one point in the PC game Spycraft: The Great Game, the villains approach you with the offer of joining their organization. If you accept you're tasked with assassinating the President of the United States. Regardless of whether or not you do it you're then killed by another assassin as payback for arresting his girlfriend earlier.
Blood Storm kicks off with the High Emperor getting assassinated, and all eight fighters are pointing fingers at each other. If Tempest wins, she accidentally lets slip that she released the Big Bad and ordered her father's execution. She is promptly overrun by an angry mob and beheaded.
In AdventureQuest Worlds, if you make the choice to betray and kill Artix during the finale of the Doomwood saga, Vordred "rewards" you by making you the very first of his new undead minions as he unleashes a Zombie Apocalypse upon Lore.
Implied in Grand Theft Auto IV, Playboy X and Dwayne are longtime friends. When Dwayne returns from prison a sullen man, eventually the two butt heads to the point where Niko needs to kill one to continue the plot. If the player kills Dwayne, Playboy calls him up and wires a large amount of money, but tells him that he has to try to kill Niko if they ever see each other again (They don't).
A more likely explanation is that Playboy X doesn't want anyone else to know of his involvement in Dwayne's death, as it would be really fishy for him to not try to kill the murderer of his "best friend".
In the Dark Brotherhood questline of The Elder Scrolls V: Skyrim, Commander Maro launches an attack on the Dark Brotherhood Sanctuary after Astrid arranges for you (the killer of his son) to be captured by him. The fact that she was the one who ordered the kill is definitely a factor in this.
Planescape: Torment has a meta-example in the Fourth Circle of Zerthimon: According to the passage, in the middle of a Githzerai uprising, a Githzerai named Vilquar voluntarily warns the illithids and feeds them as much intelligence as he can. They kill him the instant they feel their victory is assured.
Averted by Gwyn in Dark Souls. After Seath the Scaleless betrayed his fellow Dragons, Gwyn rewarded Seath by making him a Duke. This did not sit well with Gwyn's bishop Havel the Rock, who hated Seath and the sorcery that Seath created.