The problem with measuring the power of beings like the Emperor is he's a plot device, not an actual character. Like the gods of Chaos he's powerful to the point where mortals can fathom his true level of power. He's bound to the body of a human to give him the ability to fail, otherwise 40k never would have happened.
But there are always fun to talk about.
The Emperor would win the battle as he has more tools to win it with.
The custodes are better then a normal Space Marine in every regard. They are stronger, faster, and better equiped. They would utterly smash the bodyguards of the 4 Primarchs in a normal contest. The fight is hardly normal considering the strength of the fighters involved though.
The Emperor has several tools at his command and the most logical first attack is a psy assualt ment to faze or outright kill anyone he can to buy himself time. He would know the limits of Magnus' abilities so he shouldn't have too much trouble making an attack of enough power to give himself a moment of thought.
Now assumeing that the psy attack would outright kill the Marine bodyguards is kinda a no brainer, but the fazing of the primarchs may be a stretch depending on how far into chaos they have fallen. Thats where the Custodes come into play. They may not last long but they will last long enough for the Emperor to do what he needs to do.
Following the psy assualt he would attack Magnus first, as he's own psy abilites would be limited in potency while the cyclops was on the feild. Magnus would go down quick, as physical combat is not his forte, with the other 3 primarchs recovering as Magnus falls.
With Magnus gone Angron and Mort would fall the a psy attack with ease, leaving just Fulgrim standing.
Fulgrim is the wild card in the entire encounter, as he was possesed by a deamon, rather then just assending to deamonhood. We don't really know what kind of effect the assualt would have on a deamon possessing a body would have. Could it kill the now possessed Fulgrim, or would it simply stun him again and force the Emperor to destory Fulgrims body outright? Regardless it is within the Emperors power to do both so his victory is already in the bag.
Disclaimer: The above is assuming no plot devices (aside from the Emperor) were used (He loves them to much as a father to kill them

) and all parties wanted/resigned to kill the other with no moral issues clouding their thoughts. :laugh: