The Secret Meaning
Alien 3 is secretly about AIDS in the '80s and early '90s, and how badly we fucked up trying to deal with this epidemic.
The deaths of Newt and Hicks, as painful as they were, is actually central to this message. The scariest thing about AIDS (in Alien 3) is that it seems to kill almost randomly -- it doesn't matter if you are an innocent like Newt or a fit and healthy young man like Hicks; you might start showing symptoms and quickly die before anyone even knows what's going on.
Then, there's the population of "Fury" 161, an almost completely abandoned prison planet. One of the higher-ups realizes they can potentially wrangle this little alien-problem into a profit. So, they show up dressed in hazmat suits -- which is what some doctors chose to wear when they treated AIDS patients.
But, the most telling part is the speech given by the character Dillon, who explains his decision to try and kill the monster that's killing them:
"You're all gonna die. The only question is how you check out. Do you wanna go on your feet or on your fucking knees, begging? I ain't much for begging! Nobody ever gave me nothing. So, I say, fuck that thing. Let's fight it."
It's badass, and strikes the exact same tone as Larry Kramer's speech from when he launched ACT UP in New York in 1987, five years before Alien 3 was released: "If my speech tonight doesn't scare the shit out of you, we're in real trouble. If what you're hearing doesn't rouse you to anger, fury, rage, and action, gay men will have no future here on Earth. How long does it take before you get angry and fight back?"