I know this will provoke some people, but: Good guys don't murder, can't murder.
Murder is "the unlawful killing of another human without justification or valide excuse, especially the unlawful killing of another human being with malice aforethought."
What you're talking about here must - at best - be killing, because you are putting a very specific constraint on those people: They're the good guys and in our society murder will never be seen as good.
And this is not about semantics. I'm not saying "haha, you used the wrong word", I'm saying you think in the wrong terms. Wrapping your head around "Murder is good" will be hard for the reader and that IS an understatement. Any effort put into letting the MC come to realize "their murder is good" is therefore wasted. You need to convince your reader, if you really want the MC to accept the good guys as that, or otherwise the disconnect between reader and MC will be too big (unless they're sociopaths, then they'll probably be fine with murder).
So how do you convince the reader that the good guys are the good guys? That is the important question. Because if you want to explicitly define your MC as a hero/anti-hero/villain/anti-villain you can only do that by defining what is good and what isn't to the reader. If you don't, the readers will do that for themselves, in the confines of their own moral compass. And you have no power of that. They might see it the way you intend to, but I wouldn't bet on it.
The first clue to that is: How did you convince yourself that they're the good guys, other than simply saying "I define them as good guys"? That, will not do.
As an after-thought: You will never be able to create a world where murder is allowed or accepted, without the reader (violently) rejecting it. This world would be so fundamentally different to ours, that there's no other option for the reader.
Let's take a popular example: Dexter. Dexter's saving grace for many people was, that he only ever killed criminals who - in the eye of the general populace - deserved to die. For the average viewer he had a legitimate reason to kill them (not murder, phrasing). I personally hate that series, because I think he hadn't. And people, in general, who think he hadn't had a legitimate reason, tend to disconnect with and dislike him. You will never convince those people that he was a 'good guy'. And if he had killed an innocent without very good reasons, the character would've been instantly disliked by a lot of people. There's a list of "innocent" people Dexter killed and lo and behold, he always had a "good reason". Some where drug dealers or rapists, others he killed in self-defence and at least one person he killed on request of said person. Here's the link: List of "innocents"
A perfect example. The series creators had to convince the viewer that Dexter was the good guy. Not by any non-contrived scene or event, but by appealing to the viewer's moral system. The reader is the key, not the main character.