If Future Trunks were to successfully bring back Goku and Vegeta, I would think there'd be no issues at all. To begin with, Goku himself as an SS3 is stronger than Buu. He also only doesn't personally take care of the majin in the main timeline because he's dead and has faith that Gotenks will be able to kill him. It's a problem that the people who are living should take care of.

But let's say somehow SS3 isn't enough for some reason. Goku and Vegeta can still do the Fusion Dance. And if he's in a situation where he's the only one that can do it, he will, as demonstrated through the circumstances that led to Vegito's first appearance. So they'd just fuse into Gogeta and destroy Buu, who wouldn't even be remotely close to him in strength.