So with the USM Auriga being a medical research vessel, with numerous labs,containment cells, military personnel and an advanced A.I in place to monitor systems and the Earth having already been hit by the Lacerta Plague ( an unknown epidemic that was mentioned Call)....
Standard protocol if shit went down on any such medical research ship was not to have the A.I self destruct the engines, or plot a course into the sun or deep space, just bring the damn thing back to dock on Earth?
Not even hold in quarantine in orbit around it?.
The labs and holding pens for any biological material couldn't even be isolated and jettisoned in case of an emergency?
And nobody thought to put in Acid Resistant panels or glass,yet ship is supposed to have extra thick hull plating and we know it has a stealth drive.
That's before you get to fact they did not need Ripley alive for further study, her corpse could of joined the others in the statis tanks..Queen was the prize they wanted.