Perhaps, but it's also not contradicting what was already known, but rather fleshing it out. Personally, I fond it more interesting than just accepting the Guardians are good. This fits in better with our world now, which is multipolar; the Guardians were the product of a (excuse the expression) bipolar world, and this idea of one side being absolute good and the other being absolute evil(which, as I've mentioned a lot, is shot through DC's entire cosmology--think of any silver age JLA issue--and I think it's interesting Johns has been deconstructing that)is a dated concept that should be re-examined and be made more complex. Consider the war of light in light of either the breakdown of the Iron Curtain or the "War on Terror."
What the Guardians show is that those who think they're "good" and thus everything they do is "right" can cause far more damage sometimes than "evil." It's an idea that takes into account what that idea has caused in real life, all the way up to the neocons. It's this theme, examined even more closely in Tomasi's GLC, that keeps me reading the books.
My PERSONAL opinion is that the Guardians are tools. But regardless of what it makes you think of them, it's this theme and examination that has been Johns and Tomasi's greatest strength.