How does the Emperor's status as Anathema of Chaos affect the philosophical aspects of Chaos?
Well, I don't think it actually affects it. He's not a Chaos God. (Also not a God, see below.) He doesn't sit on the Axis of the Gods anywhere. He's outside it.
Crusade-era Emperor was truly the Anathema of Chaos. The Imperial Truth reduced the flow of "energy" to the Chaos Gods. Humanity still feeds them with their actions regardless of what it believes, but it was the lack of belief in Gods, and therefore the Chaos Gods, that was truly poisonous to them. Had the Imperial Truth completely and utterly taken root in Humanity, the Warp would still be there. Daemons would still be created by the thoughts, emotions and actions of Humanity, souls would still end up there. But without the
belief in the Warp and the malign sentience of some of its inhabitants, Daemons would be weaker. The Chaos Gods would not be fed by billions of souls directly worshiping and sacrificing to them. Their names might not even be known by the learned, and in the magical thinking of 40k, that's pretty important.
But that all went tits up in the Heresy.
Current Era Emperor? He's a doorstop, at best. The mythology says he's constantly doing battle with entities in the Warp. It's never been truly qualified what he's doing though, other than stopping Chaos from pouring through the webway into the heart of the Imperial Palace. I suppose the theory is that current era 40k is so debauched and violent and aware of the mystical that Chaos would have long since broken out of the Eye and flooded into the universe were the Emperor not there keeping it at bay. I'm a little skeptical of that. I mean, the Emperor is doing something. You can't be that powerful and still alive on some level and spent 10,000 doing fuck all with your time. But being the sole thing keeping Chaos at bay, and the rest of what's going in 40k is, comparatively, way less important?
That's Imperial Propaganda in my book. *BLAM*
So in order to answer whether the Emperor impacts the philosophical arrangement of the Pantheon, we have to answer: is the Emperor a God? If he's not a God then he has no impact on the alignment of the Pantheon.
And over the years I've come to the stance, like the Space Marines, that the Emperor is just a man. The best mans ever? Absolutely. Actually a mans in point of fact? The HH books go on and on about how Primarchs are human and yet not. They were accepted as human so it seems only right that the Emperor of Mankind gets the same classification, regardless of how he was created or whatever weird shit was woven into his existence to make him more powerful. And to be honest, in my mind, the Emperor being a Man at the end of the day only makes him more badass. To know it's still just a man hooked up to the Golden Throne that has been struggling and suffering for 10,000 years and still hasn't given up. That's true to the spirit of HUMANITY FUCK YEAH.
Making him a God seems like a cop out in comparison.
So I see the Emperor as outside the Pantheon, and not even divine. The Pantheon existed before the Emperor and it didn't suddenly change the moment he woke up. In my mind the Pantheon isn't like, written into nature. It's not like Fire, Wind, Water, Earth. The Pantheon is an ultra exclusive club of Warp entities who became such focal points for the most common emotions and desires of living beings that they became elevated to Godhood in the Warp and whose reaches are so vast they can touch each and every part of reality. And the Emperor, essentially a max level multi-disciplinary wizard to put it in D&D terms, figured out how to parlay with them and cheated some of their power away from them.
So the balance and philosophies of the Pantheon aren't like, immutable facts of existence, even though in the text and in our minds they're built up to be such and they're seen through the lens of Humanity. There's some writings out there of Xenos races that understood the Chaos Gods and the Warp but their overall take on it was different. And were all the traditional races of 40k to be snuffed out and new, unique races to be inserted, you'd see the balance of power in the Pantheon shift. New gods might be born with different priorities and spheres of influence. (One of them might even not be a total bastard.)
The answer to that question comes down to your own personal outloook: is violence, the hunger for knowledge, desire and decay fundamental parts of all life, no matter what race or creed? If so then the Chaos Gods will always sort of be there until there's nothing alive left in the universe. And signs do kind of point to that being the case. At least, for 40k.