I believe that if Chaos as a whole, using Horus as their Avatar of Chaos after he went through the Warp Portal of Molech. Though those that accompanied Horus to Molech only noticed that he had gone for a few seconds before he reappeared, looking very old for a Primarch. After personally beating and conquering the armies of the warp himself for thousands of years and earned the power that the Emperor tricked from the Chaos Gods. Then guys lets face it. In the Warhammer universe it is widely believed that there is only war. False, during times of war. Only certain sectors of the universe are actively engaged in this. The Imperium is suppose to be Trillions upon Trillions, this means that only a tiny tiny fraction of their numbers are fighting at any one time.
This brings me to the point. If a Suped up Primarch such as Horus imbued with powers of Chaos Undivided no less cannot kill or beat the Emperor. (Who is worshipped by Trillions) Khorne is not as powerful as you believe, since war in the 40k Universe is fragmented, who is going to win. Khorne with a billion deaths? or The Emperor with Trillions of followers?
My personal belief is if the Emperor can make the Chaos Gods flee with fear when he summoned his own warp powers to erradicate Horus the Emperor will win.
Sure he may not be able to use his psychic powers against Khorne to wound him or defeat him but by the same measure of his power. Surely the Emperor can use his own powers to enhance, his already perfect being to overcome Khorne in close combat.
https://www.reddit.com/r/respectthreads/comments/2jxqaq/respect_the_god_emperor_of_mankind_40k/
The thread above, contains general overall feats for the Emperor.