No, Darkseid can't Kill Buu, he doesn't have the power to totally break up his atoms. Buu can come back from being blown to every bit as long as something is left and Darkseid doesn't use power that explodes any being like that.
I have seen this develop with interest. Two of Darkseid's powers can take this, and he doesnot need to kill Buu to do it. That is the point you have not been coing at since the start of the discussion.
1) Omega Effect, Among a variety of effects, one of them is Instant transportation, to a prison dimension of Darkseid's design. Now you may debate that Buu, capable of time warp can bust out, but a piece of cake it will not be. While he conveniently knocks himself cold trying that, and even when he gets close to coming out, Darkseid's vested interests will be in not destroying a power source like that, but to keep him put and use it in his experiments. Lets not forget that he has conveniently done this to another being billed as more powerful than Superman, the Cyborg Superman, who is primarily composed of energy. Seid trapped his essence, instantly manipulating his form into a more easy to handle capsule. This is also a power, that DC has less revisited, because simply put, it will be the end of Darkseid’s opposition, even before a match up occurs. The hook is that, the beam connects with anyone it is intended to, so there is technically no running from it. With a less mature specimen like Buu, we can not expect ‘smarts’ over Seid in a battle, or just lain matching of the wits.
2) Omega Sanction: Upon the remotest ‘connection’ with its intended victim, the beam scatters the victim’s personality, splitting it into several realities, each billed as ‘worse than the other’. Hence, another power that DC might or might never visit in the ‘re-launch’ universe, but which will forever be a part of Darkseid’s mythology. There is no escaping it, no turning it, and no way out of it, expect to succumb to it, and spend a lifetime depending on the state and control of mind, to get back to the one primary reality where it all happened last.
Knowing Buu, either of those 2 tools are too much for someone of his mentality to handle. Even the more mature Buu, is ‘immature’ and full of bravado, as I earlier stated.
Superman, or even a lesser being might have stood their own against Darkseid, more due to their will and drive, rather than their powers. Inspite of agonizingly poor writing, Darkseid remains one of the most powerful and manipulative figures in comicdom.
Factor in his immense backup resources, (like a motherbox, that in a well written comic story, instantly effects healing or a counter measure) and Buu has no prayer to win this.