One of the reasons I enjoy the fact that Aliens basically has WY completely unawares of what went on, and has Burke acting out of his own personal greed. It plays against expectations just like Bishop does on a first viewing.
I agree with this, the first three films portray the company in a morally grey light, for all intense and purposes, its just a company and one that has become interested in an alien life-from which they hope to acquire which is in contrast with the silly blatantly evil corporation of Alien Resurrection and most video games, who go around killing people left and right and happily use people as hosts for Xenomorphs.
In the first film, they don't want anyone harmed, but the specimen's priority is higher than the crew and the android Ash then makes its own interpretation of the orders, especially when the humans seek to kill the Alien and acts accordingly (similar to apollo). In the second film, I believe Burke was acting alone, and third film has W-Y make an offer to Ripley, they may have even gone through with it (we will never know), they never killed Morse either when the jaded Ripley believed they would kill witnesses. However, A:CM then has Michael Bishop as a total sociopath who kills people no longer useful to him.
The novelization actually casts The Company in a much kinder light where WY never wanted its crew to die but had hoped that the crew would be able to live through the entire voyage with the Alien alongside so they could pick up their paychecks back home.
I don't remember the novel at all and I don't think it's over that Ash is making the decision himself in the movie - I think Parker says "It's the damn company" (after "Ash is a god-damned robot!"? - I'm sure there are folk on here that know the movie line by line, though!)
But "the damn company" seem to be at the core of it and Ripley gets pretty shoddy treatment in Aliens as well.
However - I like the idea of making the company grey as opposed to black. I work for an evil corporation (I really do), but not everyone that works for the Company (see what I did there - capital C yo) is a corporate bastard who'd f**k you over for a goddamned percentage. Some are, but most aren't. However, decisions have to be made - in the case of Alien, WY are seeking a competitive advantage (though I've always asked the question "What could you do with an alien in terms of a bio weapon?" I guess the answer is "They didn't know it can't be controlled" (though Ash's "purity" monologue puts that on shaky ground)
But the idea that not all sci-fi corps are evil is a really good one and plays against the expectations (as you say) set up (intentionally or not) in the Aliens movies. Obviously, ts a theme with many future worlds (OCP, Tyrell, Soylent etc) so it'd be ace to see something that plays against that.
I'm a big advocate of a TV show for the Aliens 'verse and in that sort of set up, you really could get under the skin of that side of things?