Kal and Walon are mercenaries hand picked by Janga Fett to train the commandos themselves, they have NO alliegance with both the republic and the jedi. Clones are synthetic Mandalorians, but still ARE mandalorians, and we all know Mandalorians would rather fight for their "brothers" rather than the republic. The clones are still human, still having the ability to feel emotions, and prioritizing duty and brotherhood is one of them. And Kal, being the compassionate epitome of being mandalorian, unleashes their feelings of mindless duty and shows them that they arent mere robots/slaves, they deserve a REAL full length life instead of being used as weapons only to be discarded right after. Just look at Able-1707 he actually helped the rebellion against the empire, so i dont see the reason for the clones not to fight for themselves and have their own agendas. As long as they have emotions they have the chance to go "rogue" (somewhat portrayed in the game by cowardice clone in the second chapter, he ran and hid caused by survival instinct) for personal reasons.
Yes at the end yoda does speak of "greater things" but we all know that jedi arent as wise as they portray themselves to be even in the movies the jedi council is betrayed, if jedi can do it, i dont see why clones cant. and if you havent noticed Niner, Scorch, and Boss have certain doubts in their voices. This is the turning point in their mentality TOWARDS the republic, the Mandalorian instinct to FEEL for their brothers rather than just be squadmates. Sev is the missing part of their pack, they cant just kill him off, THAT would be too cliched, especially in a star wars themed storyline. Even though the happily ever after thing is too :P but hey they were bred to fight for a war they didnt ask to be in, raped with training at an early age, sent off in packs to die, and when they get home they are just naturally killed off, i think thats a bit of a nomination for a good reward such as that