I'd be fine with a fully remastered original interpositive in high definition with the theatrical audio, as Blade Runner did. But yes, it is better to go the negatives.
Speaking of which, I'm curious as to where the new Apocalypse Now theatrical cut transfer will come from. Its a brand new HD transfer, in the full widescreen for the first time, but the negative was cut up for the 2001 re-edit.