Yeah it does seem like FOX forced their hand on including Alien3 in their "canon story."
When Hicks and newt died, it was sad but so were the deaths of everyone else in the first two movies. Except for Burke, lol
I don't hold it against them for killing them off instead of keeping them in the third movie. That's the direction they decided to take, and the movie as a whole stood up on its own. I loved Alien3 back when it came out in the theater. It was a solid movie.