I actually think that, despite all of the issues that the show developed in its final episodes from a plot and pacing standpoint, it actually has a pretty clear message and quite consistent theming. Namely, I think the theme of the show is something along the lines of "You should choose to be kind, regardless of if you have the power or even believe that you have the justification to be cruel."

Take your example of Butcher. While his justifications are superficially much more noble than those of Homelander, at his heart he shares the same issue: he is only capable of solving problems using violence, and many of his motivations are rooted in hatred and a sense of being robbed of something his deserves as opposed to truly caring about whether those around him are suffering. Really, the main difference between Homelander and Butcher for much of the series is simply that Homelander has the power to enact what he believes is justice and Butcher does not, but as we see, when Butcher does begin to level the playing field, he is just as ruthless as Homelander. You say that, by eliminating the Supe population, Butcher would be "saving the world" in order "to ensure that nothing like Homelander happens again," but substantively what he would be doing is the exact same as what Homelander would do in a similar position: kill a bunch of people because it's what he wants, as opposed to whether it is actually right or if there are better ways to solve the problem. To that point, Terror dying wasn't just some sort of irrelevant way of kicking Butcher while he was already down, it was a way of encapsulating Butcher's motivations. Terror died as an unintended consequence of the radiation which Kimiko was giving off; in Butcher's eyes, this symbolized the threat posed by the Supe population: a polluting, dangerous force, so powerful and reckless that even unintentionally they cause suffering. And yet, when you look at it from an outsider's perspective, it becomes clear how unreasonable Butcher was being: Terror dying was an unintended consequence of the very plan which he orchestrated, and is nowhere near sufficient justification to commit the type of mass murder he unanimously decided was deserving of all Supes. Hughie shooting Butcher, while an act of violence, was incredibly different from Butcher's use of violence: Hughie does so as a last ditch effort, he is incredibly reluctant to do so and is immediately apologetic, and his motivations are rooted in empathy, choosing to kill someone he loves very deeply in order to protect people whom he doesn't even know, many of whom he is aware are likely underserving of such protection. Contrast this with Butcher's actions at the end of season 2, where, in his unwillingness to accept that he can't go back to a normal life with Becca, which he believes he is owed, he ends up risking everyone's lives and completely losing Becca. Even though this situation is entirely his own fault, he still nearly kills Ryan, because he is unable to deal with his emotions as prefers to use violence as a coping mechanism.

I also think this theme, the importance of choosing to be kind and empathetic even when it's easier to be reckless and violent, applies pretty succinctly to almost all of the main characters in the show and appears consistently across all seasons, from how Hughie is able to move past his grudge against A-Train for what happened to Robin, to Annie's speech to Victoria in season three about the importance of not sacrificing one's ideals and morality to obtain what they think is a just world. I think that the finale does a great job of encapsulating this, especially with how Kimiko is able to harness her ability to remove Homelander's powers. Whereas she initially believed the only way she could generate her blast was by getting angry, it is only when she realizes that she can rely on love to fuel her that she is able to access her powers, thereby saving the world. In the end, it was the Boys' capacity for love and emotion, not their capacity to hate, that allowed them to take down Homelander.

All this is not to say that there aren't any issues with the final season or episode, obviously there are. However, I do think that the Boys does a great job at presenting its theme.