That depends how do you define "the control":
Let's start from the religion: Emperor wasn't opposed the worship by itself - he was worshipped as a various religious figures during the Earth history (he was for example Saint George), but he was forbidding it, because superstitious people could start believing in wrong things empowering Chaos Gods.
Currently he NEEDS to be worshipped - the faith of the billions gives him enough power to keep opposing the Ruinous Powers while at the same time controlling the Astronomicon and well... staying alive as a rotting corpse.
As to his control over Empire - in his current state he can't be involved much in the day-to-day functioning of the countless planets; all he can do is affect the minds of people - hence the vast number of saints, prophets, heroes etc. But it's obvious, that he is not happy with the situation of his people - there was a galaxy wide event around 500 years from "now" (so around 500.M41) where almost every people in the galaxy had a dream about Emperor crying.
If you are looking about a case when he indeed still affected the fate of the Empire, please look at the story of the Age of Apostasy:
The High Lord of Terra Goge Vandire usurped the role of the Ecclesiarch and declared that he has been blessed by Emperor himself. He gathered vast power but in his madness he was ready to torn the Empire apart. To prevent the incoming crusade of loyal forces against Terra, Adeptus Custodes (Emperor's personal bodyguards) invited five Brides of the Emperor (Vandire's personal bodyguards) to the heart of the Imperial Palace. There, they've talked with the God-Emperor himself, after which Alicia Dominica and her vengeful Sisters confronted the corrupt Vandire within his own chambers. Vadire was killed with a single stroke and his Reign of Blood ended.