I don't know whedon's first script.
But bringing Newt back through cloning makes no sense because she didn't have a queen inside her. So she is completely worthless to the company.
Wasn't there even a plan to dismiss Alien 3 as a nightmare episode?
Well, I mean long before Blomkamp appeared on the scene.
(His plan was a new Alien 3, so to speak, with Hicks, Newt and Ripley)