With many here celebrating that this "wipes away" the canon of the AVP films, let me share my thoughts. No official canon is truly gone until the franchise owners say so (FOX). As is evident with the Star Trek reboot, creating a canon contradiction does not eliminate canon, it creates an alternate canon. For example: there are multiple, contradicting plot lines in the Terminator franchise. And even though the new Batman films are extremely popular, they do not destroy the canon of the older films, they simply create alternate canon. The point could be made that since the filmmakers have stated that Prometheus should not be regarded as an Alien film, that it's doing its own thing, that AVP would be part of the "traditional" canon, a true Alien film, whereas Prometheus would essentially be a reboot or spiritual successor to Alien. This would create an alternate "Prometheus" canon in which the other films are only taken into account in the lightest sense. On the other hand, you could argue that AVP started its own new alternate canon that was never meant to be considered part of the Alien franchise, and that Prometheus is the true Alien film.
Considering the expansive franchise that Alien is, there is so much material with the primary films and EU, I think it's fair to say that canon will be slightly different depending on what stories of the franchise a fan prefers. Many Alien fans don't like to consider Aliens canon even though officially speaking it is. The same is true for the AVP films, even if Prometheus has such a contradiction with the AVP films to make them completely incompatible, that does not destroy the canon of the AVP films, the contradiction simply creates an alternate canon. AVP is still official canon, just a different canon. You can never please all of the fans, and many here, even if they are not outspoken about it, are fans of the AVP films. Debate on which films are better or more relevant to the franchise is to be expected, but I'd like to suggest not alienating (pun intended) fans of the AVP films. This is an AVP site after all.