@biznizz
You basically explained why I see it as Brau doing "the dirty work". The dirty work in this case is destroying / killing whatever is deemed to be evil / guilty / other / uncivilized / unacceptable in society / etc. As you point out, at least from Atom's / manga author's perspective, the President was not deemed evil enough to warrant death. Perhaps his actions could be understood / justified in some way. Perhaps he can be rehabilitated and still have a place in future society. Perhaps he just no longer poses any threat.
Roosevelt, it seems to be suggested, would not ever change and would always pose a threat. And indeed his level of threat would be far more dangerous than what any human, even a president, could impose on the world. Plus, the author and many characters seem to have decided that "the buck stops" with Roosevelt. That is to say, there he is the root cause of all the other evils in the story.
But, Atom did indeed say "nothing can be born from hatred" and it was repeated a couple times to make a point of it. It's as I say a "love conquers all" sort of message. In the face of hatred one would face it with love and kindness rather than meeting hatred with hatred (which Atom did briefly toy with in the Pluto fight). And indeed, Atom did apply this with Pluto.
This is in contrast to a traditional hate vs hate, "good" beats down "evil" type scenario in stories.
However, what to do (in a story or in real life) when the "evil" (in this case Roosevelt) does not get won over by "love" and instead he still wants to follow through with his plans? Either the person espousing "nothing can be born from hatred" must become a hypocrite (only showing love to those that do as one wishes) or that person martyrs himself or that person is conveniently saved by someone else doing the "dirty work".
Thus, Atom gets Brau to kill Roosevelt. Atom does not have to sully his saintly, innocent image that denies any value to hatred because anyone in universe (and anyone not reading too closely) his message "nothing comes from hatred" seems consistent. And he and the world get to live in a world free of Roosevelt thanks to Brau who does not subscribe to any such philosophy. Indeed, it is thanks to Brau's "hatred" that the world has a much greater degree of peace and order. Something came of hatred after all.