The Orks - or, the Krork - were a genetically engineered race developed by the Old Ones to fight the C'Tan, specifically, Nightbringer. As Orks love to fight and are immune to 'the fear of death'.
Similarly, the Eldar were created to fight the Necrons, being heavily psychic, that didn't work out too well since Necrons laugh at silly Warp Users. So, the Old Ones moved to Plan B - the Krork. All this is from the 3rd Ed. Necron Codex. As both Orks and Eldar were created by the Old Ones, it's heavily implied in Xenology that the Eldar and Ork Gods are one and the same.
The two major Gods left being Khaine and Cegorach - the Laughing God. Who are analogous to Gork and Mork.
It's also implied somewhere (I can't remember), that the Emperor is the greatest weapon against Chaos that the C'Tan have. What!? The Emperor is a C'Tan weapon!? Yes. Or it's at least implied that He is.
...It may also explain why Cypher is so keen to get at him. Since he's also an agent of the C'Tan - or at least he used to be.