I think the reason this rubs some parts of the fandom the wrong way is because of the psychosexual components of Giger's stuff. The fact he's been reported for a good long while as having no more impact on the film than designing some murals, already gave people an impression that the hoped for return to those halcyon days of 'what if', might never come to be. If given the choice between Giger having major contributions to the designs and tone of a film and it being directed by Ridley Scott? I'd almost put money on at least two thirds of fans voting enthusiastically for the Giger option.
A 15 rating is a double-edged sword. You can imply a heck of a lot with ambiguity and I've always used Lambert's death scene as an example of this. It's probably the most disturbing of the entire series and much of that has to do with the audio heard over speakers, reminiscent of an agonising birth, immediately after that worrying implication of a tail slowly creeping up between her thighs. But... There are also a lot of films with a 15 rating which are awfully tame.
I know that Ridley Scott's repeatedly said he wants to scare the shit out of people, but we still don't know what his standard of 'scary' is, these days. He might have gone down the path of people like Moffat, in charge of today's 'Doctor Who', who maintain that the scariest possible things are often the most mundane. Hotel rooms, darkness and so on... It's totally plausible that we might get a version of 'Prometheus' which is very inferior, horror-wise, to the kind of subject matter implied with 'Alien'.
As always, time will tell. But I think we might be jinxing the thing by heralding this as the most awesome possible thing to happen for the project.