Of course if you are to put charity ads in the game, you'd have to get permission first. Goes without saying.
As for how to implement them, though, that's a different one. And to be honest, I think Coruscant Red Cross/Amnesty Interplanetary/whatever ads in an SW game would just be silly. It's bad enough that they speak American/British English and live on Earth-like planets if they aren't going to have Earth's organization's, too.
Everything has its place. I've got nothing against charity (I'm a Red Cross volunteer, for crying out loud), but if you're going to include it, include it in opening clips, etc. Play a short Red Cross or Amnesty or Animal Shelter ad before the game starts and I'm fine with that. But during the game? No.
And as a side note, SW seems to be 100% free of ads anyhow, at least in the Civil War, so however you put it, it'd be out-of-place.
"One of the bitches actually gave birth while she was attacking, and her puppies joined in on the carnage."
--the awesomeness that is Boatmurdered.