I think Sigourney Weaver generally wanted to be killed off because as she said the formula of her being the only survivor and no one would listen to her was starting to get a little worn out.
The only time I saw Sigourney mention her disinterest on Alien VS. Predator was on a behind the scenes interview of Alien Resurrection and she mentions she was killed off in Alien 3 was partly because of the repetition but also because of the rumors of Fox making AVP.
Clip here, star at 3:33 – 4:22
https://www.youtube.com/watch?v=ncAhHeUSdsU&list=PL20F0F6185A9A2FAAWhilst she was interested to return if either Scott or Cameron were directing. And they were both intending to work together with her on a fifth Alien during the early 2000's. However Paul W.S. Anderson's Alien VS. Predator pitch killed that project.
As we all know Ridley Scott would return to give us Prometheus. I guess Sigourney and some Aliens sans cannot take the concept of a cross over seriously believing it undermines the integrity of the original films. Examples such as Frankenstine Meets the Wolfman, King Kong VS. Godzilla and other Toho Kaiju VS. movies, Freddy VS. Jason while entertaining to some weren't the most well critically received.
I guess some would see it as a desperate attempt at taking franchises that have run out of steam and mixing them together to milk the last few bucks out of these cash cows. Cross overs/ co-existing movie universes can be genuinely good and expand upon a movies mythos.