Predator 2 has a xenomorph skull in it but we don't call it an Alien film because its part of the Predator franchise. Alien has a space jockey corpse in the film even though the film is clearly not about space jockeys.
With that logic, you can't call Prometheus an Alien film just because there is a dead space jockey in the movie. If it's about jockeys, then its also the beginning of a new franchise and/or stand-alone film.
There is your logic right there.