I don't see why people have so much trouble with this. You can discuss "what ifs" all day long - "what if Sloane is not so bad but is merely misunderstood?" - "What if Reyes is actually a dictator in the making?" - "Who tortures more?" - "Who uses more dirty tricks?" - we can't answer any of those questions. At the end, what matters are the facts we know.
Sloane never lifted a finger to help you, remember this. She keeps saying how much she hates the Initiative. If you do the "honorable" thing and save Sloane, she literally asks you for a "protection fee or else" when negotiating for the outpost. She continues to flood the streets with drugs. She continues to beat people up who don't pay up protection fees, and those who can't pay up, she sends them to die in the badlands. She lives in a throne room where she hosts parties while people outside are dying. She wants to be in charge. Drack tells you how she always had such tendencies, so she has a history with such things. All of this is a really big indicator that she only cares about herself and will take actions at the expense of others to stay in power. Therefore, she is not reliable, nor trustworthy.
Reyes went through great trouble to help you. If you let Reyes kill her, all of the above problems stop. Like, you can actually go to the city and see it with your own eyes, the problems stop. On top of that, the Angaran government takes over, bringing stability and welfare for the inhabitants, something the inhabitants desperately need. This shows that Reyes is prepared to make compromises with others, it's not just all about him. The Initiative will get political browny points with the Angaran government, so the Initiative benefits too. Reyes said he wanted to show you his true self before announcing who he really is, but he didn't really want to lie to you and he apologizes for not being truthful sooner (his story is backed up by that Angara leader woman). Reyes says he wants peace and fair trade, which are promises he fulfills. So, he has shown integrity, goodwill towards all parties, and trustworthiness.
However, Reyes also mentions he will be pulling strings from the shadows. That might sound scary, and it's not ideal, but you must remember how much the inhabitants, the Angara, and the Initiative have benefited from his actions. Also keep in mind that Sloane was already doing the exact same thing and think about how hurtful Sloane's actions have been to everyone (except herself and her thugs). So, at the very least, if you see this situation as having to choose the lesser of two evils, Sloane is clearly the much bigger evil that has been hurting everyone, while Reyes is an evil who goes out of his way to make others benefit and he plays nice.
That said, I just want to comment on how silly the writing of the final showdown was:
"Hey there, stranger. I know I've been treating you and everyone else like ***, but can you do me a really, really big favor? I'm going to this secret meeting, in this cave that is really hard to escape from, where people will surely want to kill me, and I need you to save my life. No, I won't take my most trusted body guards with me. You, stranger, will be the only thing that will stand in between me and my enemies. And you know what? I think I'll leave my shield right here, I probably won't need it... Let's go."