He's already said that after speaking with Ridley Scott about the 'Prometheus' sequel, some of the ideas had to be removed. It's most likely that this was to do with any Space Jockey-related elements.
Of course with Scott producing, he isn't gonna step on his toes, but this makes any attempt at a retcon of A3, seem even more cheap than before.
Honestly, does anyone really think PROMETHEUS was better than ALIEN 3?
I like PROMETHEUS just fine (provided we get a good sequel) but its still the 4th best film in the franchise.