Time will tell whether Mitka and Aric made the right choice or not, but they're facing a situation where they are getting orders from obviously corrupt people who are more concerned with public appearance and covering things up than with what is actually good for the Republic.
They don't join the Empire, because they're even worse, so they takes the best choice available, one that has a chance of protecting the common people and giving them freedom. It's not a clear cut decision in terms of right and wrong, but then it's pretty rare that you actually encounter pure black and white choices in general. She and Aric are making the best choice they can with the information they have.
They're in the Army. Unless they've got generals stars hidden somewhere, they don't get to make those decisions anymore. And even Garza (horrible example that she is) is on a short leash, as she answers to the Senate. They may be a corrupt pack of lazy cowards, but they're still the ones in charge. The authority that everyone from private to general swears to follow, and the laws they swear to uphold. If one has a problem with the orders coming down they can a) find legitimate workarounds b) leave the military if their conscience is on the same level of a pampered civilian and c) shut up and get on the bounce. In short, if one can't make themselves carry out the mission, or carry out legal orders, than one shouldn't be in the military to begin with, because idealism gets left at the boot camp entrance.
And finally, who the hell gave Mitka (or any other Havor trooper PC) the pull to make that call? In lieu of orders soldiers are to either hold and keep doing what they're doing, pass it up the command chain, or kill something. Not suddenly decide they have a better idea.
As I said with my last critical review, Earthmama is a good author, and I'll keep reading. Just be aware that by now I'm hoping for what most others would consider a horrible ending.