While on paper, the new CGs appear to give the option of removing an Engineer, and the massive impact that would have on the Engineering stage, Fdev have decided only one side shall get a super special rare piece of kit you can't get any other way, while the other is just expecting you to be loyal. So, of course everyone will flock to the Engineer's faction's side.....
So much for actual choice.....
And before anyone mentions that the Empire will lose a single system, in the grand scheme of things, does that really matter? Happens all the time in regular BGS, and barely anyone bats an eye.