The church staes that the Emporer is devine and that the Omnissia and Him are one in the same, but what if a culture believed in a pantheon of gods and the Emporer is the head god?

Would this be Heresy?

The church has Saints who are revered and so too are the ancesters and Primarchs.

The Creed allows for almost any variation on the basic theme you might come up with. The only real requirement is that you revere the Emperor above all and accept that humans rule, demons/mutants/xenos drool. The attempts to fit the millions of local customs in to the Imperial Creed framework actually seem to be more about making life easier for the priests than anything. Some feral-worlder who hasn't even grasped stellar centrism doesn't have the slightest idea what you mean when you tell him that his people's Great Sky Father is actually an undead invalid on a planet half-way across the universe. Nor does he much care. But by fitting that belief into the Creed, the Ecclesiarchy has an 'in' with the people - making it easier to control them and doing away with the bother of wiping them out as heretics. Similarly, you promote one of their less offensive local gods or culture heroes to Sainthood to make them feel like a part of the greater whole of humanity.

Take the Omnissiah, for instance. The adherents of the Machine Cult may or may not really believe that He is an aspect of the Emperor (or vice-versa). The important thing is that the Ecclesiarchy has given the Omnissiah a basic stamp of approval which lets the Imperium continue to use their "blessed technology" and gives the Adminstratum license to tax them heavily.