Generally, these characters are a bit more intellectual or philosophical than the common grunts of the organization and has an understanding of the underlying belief system and would know what is right and wrong... and that the organization has been steadily losing it's way.
One example I love is the character of Dinobot in "Transformers: Beast Wars" who is a Predacon turned Maximal (happens in the two part pilot). In the show's lore, Predacons operate under a moral code akin to Bushido or Chivalry. Most, like the leader Megatron, only pay lip service to the code... but Dinobot is the rare person who follows his code and does not engage in combat with enemies that are disadvantaged. In the first episode, Dinobot shows Megatron evidence that the planet they crashed on is not Earth (it has two moons... big clue) and challenges Megatron to a dual for leadership of the stranded crew. Megatron not only refuses the dual, but has Scorpinok, Dinobot's underling, launch a surprise attack on Dinobot and leaves him for dead. While Predacons do believe that treachery is not a bad thing (underlings are supposed to betray leaders they feel are acting in appropriately... leaders are expected to be wise enough to anticipate and out maneuver these occasion attempts to grab power.), Megatron was not honorable in how he conducted himself.
When Dinobot challenges Optimus Primal for leadership of the Maximals, however, Optimus agrees, despite Maximals not being honorbound like predacons, and bests Dinobot in one on one combat despite having a 4 to one advantage if they decided to just kill Dinobot. When Optimus has Dinobot at his mercy, he doesn't kill Dinobot because that is not the Maximal way. In this, Optimus not only demonstrates to Dinobot that he is a leader who respects the ways of others, but that he follows his own code of ethics. While there is a difference between the two codes, the fact that Optimus Primal has a set of rules he chooses to live by and stands by them and is thus a worthy leader.
Interestingly, Dinobot's foil throughout the series is not a Predacon, but a Maximal ally, Rattrap. Rattrap is a loyal to a fault Maximal, and makes it clear that all his choices are made on the logic that he does not believe the Maximals are capable of being or doing wrong... thus, if he fights dirty, than it is justified because he is fighting dirty for the Maximals' benefit. Ironically, Dinobot and Rattrap both betray the Predacons and the Maximals respectively twice between the series and it's sequal series. However, their motives for betrayal are not the same. Dinobot is awakened to the dishonorable behavior of Megatron in both occasions and his honor demands he shall not benefit from dishonorable behavior. Rattrap, on the other hand, in both instances, betrays the Maximals because in the circumstances, he believes his treachery will benefit the Maximals.
It's important to note that as their interactions progress, it does become apparent that the criticism of each other is largely a mask for their true respect. Although neither would ever say it, they both come to respect the other, and their insults are only insults from their own point of view... that is, Dinobot's insults of Rattrap's dirty fighter habits and fanatical loyalty to the cause are compliments to Rattrap while his criticism of Dinobot's continued pride in his predacon morals and heritage is a compliment to Dinobot. The acknowledge that neither of them are ever going to change and their "hatred" is because they are two stubborn to admit that while they both don't respect the choice, the respect the other's conviction.
In Dinobot's final episode, all of this comes to bear. Having betrayed Megatron for the second time, and finding the trust of his Maximal allies wanning trust, Dinobot is scene contemplating suicide. In doing, so, Dinobot uncovers a plot that would, if successful, complete Megatron's goal of rebalancing the power between the two fractions and benifit Dinobot. However, said plot requires Megatron's eradication of a species that would evolve into modern humans to succeed. As Dinobot sums it up, he can choose to not act, and in doing so loses nothing... or he can act to save the humans and lose everything. As he states, his honor as a warrior commits him to act to save the proto-humans, knowing that he will not survive the battle... but to not act is to deny everything he believes of himself. Only he would know if he choose to act... but that is enough people to know he was not true to who he said he was.