This is why I hate prequels.
Even discounting the age the prequels were made. It still makes no sense for the original films to say
"We can have giant space ships that do all this magical stuff, and have all this advanced technology. And cryo tubes that keep you ageless for almost 60 years, but we don't have the technology to detect a biological contaminant the size of Vern Troyer".
All it would've taken, was a 30 second scene where she and bishop are at a terminal. As the camera slowly moves, the dialogue goes something like this.
Yes. The damage appears to have been total.
And the Alien ship?
Gone. (some jargon about depth of blast penetration and heat intensity)
And the ship is clean?
All scans over the last 24 hours have come up negative. If there were something still here with us, the computer would've found it. We're safe Ripley.
We see the weight fall off Ripley's shoulders. She's avenged her crew, eliminated the aliens forever, and has a chance at a new life. Fade into the cryo scene. That's all it would've took.