You posted while I was mulling my post. Yes, I'm bothered by "the dark side of the Force." It's more Manichean or Gnostic than Christian. Fortunately, it's vague enough to slip by most people without much effect. I don't think the intent is malign, as with Pullman.
I had to chuckle when I read your post. No, the Force was never meant to be malign, but I will admit, the STAR WARS universe has changed a bit over the years. Die-hard fans (Force Freaks) know all the discrepencies, confusions, and ins and outs of the series' evolution--oft times better than most of the employees at Lucasfilm.
My kids think the whole Force thing is silly.
I see it as drawing more from the Oriental philosophies and their condept of balance in the universe (yin and yang and that sort of thing).