The CNN article is fascinating, thanks.
I don't see how Alien3 has any bearing on the Derelict - the CMTM directly takes it into account, in fact.
As for AR, that's a stronger case but I don't think it's bulletproof, and easy to work around (your quarantine idea, for example). Even the WYR is ambiguous aside from saying it's not a viable source of eggs as of the book's position in the timeline.
I think the RPG being ambiguous is a very fair way to handle it.