That's something of a central concept in the movie: that the truth is revealed in increments, and that the early partial revelations don't really solve the moral dilemmas of the plot, they merely mislead our heroes.
Directly asking the Ba'ku is something our heroes could have done had they known all the facts. But there's no point in asking for the permission to use the Fountain of Youth when a) you don't know you are permitted to even talk
to these people because you mistake them for primitives, b) you don't know
the Fountain exists, and c) you are being lied
at by the evil Son'a and the misled Dougherty, so you don't even know who your real enemies are.
The Son'a were the only ones who knew all the facts, and they didn't want to give the Ba'ku the chance to say "yes". And the heroes, or Dougherty, or the UFP Council never reached a point where they could have asked the question.
The Ba'ku still don't get too good publicity here, as they are first revealed to be illegal squatters, then to be sitting on the Fountain, and finally heard saying they just plain won't leave. Selfish bastards, the whole lot, and not really worth the sympathies of the audience. But Picard doesn't know quite as much as the audience does, so he never gets around to hating the Ba'ku.