I agree with the racism in the pseudoscientific hypotheses of ancient astronauts in real life, but I don't think that was Ridley's intention at all. The man just used the trope to tell his story, like Anderson did in
AVP.
The concept doesn't bother me at all when it's used in fiction, like in
Quatermass and the Pit for example.
Regarding the Space Jockeys (or Pilots), there is no damage that cannot be repaired with future instalments; as happened recently with
Aliens: Dark Descent or even the
Alien RPG from Free League.
Personally, I like Engineers. They remind me of those creepy humanoids from Giger art, and I think they can subsist in the same universe with the Space Jockeys as separate entities.