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.