Actually, the Engineers would more accurately stand in for the Elder Things, though the Engineers bare no physical resemblance, the Elder Things nonetheless were genetic engineers and kick started life on earth. As such, the story thus far hasn't really negated Lovecraft's central premise at the heart of his mythos, regardless of how the Engineers turned out. The Engineers' "God"; if truly dark and terrifying, would undoubtedly restore that overarching thematic dread.
As far as David creating the classic beast is concerned, yeah I share your concerns, but Haag gave me reason to suspect it won't be so clear cut. Any process of demystification will always be hard, especially with a fairly unforgiving, established fandom, but if it turns out that David is merely re-creating or re-animating a process some Great Old One already performed, I'd be fine with that. I don't see Scott messing with the grandeur of the original Derelict scene other than perhaps providing more context, but nothing more. It all remains to be seen!