So... you agree but you disagree?
Neither. There's nothing to agree or disagree *with*. As I've already stated, what you said was irrelevant to my point.
Just because Stardock helped with developing the game itself, doesn't mean they had anything to do with helping write the lore for it. It would be a little like saying (to borrow another sci-fi example) that the special-effects and make-up personnel for the various Star Trek shows & movies contributed to writing the scripts as well.
Do you really think that's a coincidence?
Actually, yes I do. There's a large, but still finite, number of tropes/themes common to science-fiction, so it's really not that odd that both universes might borrow a page from the same "book" (if you'll excuse the somewhat tortured metaphor).
Not that I'd be entirely surprised if it turns out Ironclad was partially inspired by the GalCiv storyline (assuming Brad or someone else at Stardock leaked a little bit of the GalCiv lore to them). On the other hand, it's very possible -- if not likely -- that Ironclad had already come up with the rebel factions on their own; we can only guess just how much of the Sins storyline they'd already written when they joined forces with Stardock.