Shouldn't the trillions people worshipping the Emperor cause some massive feedback in the warp?
It's possible, but the ten thousand year time frame doesn't really factor in the millions of years worth of power the Chaos gods have been able to feed off. Also worth mentioning that even if the Emperor is the subject of worship, the myriad of Imperial worlds all interpret the Imperial Creed in different variations.
On top of this, regardless of worship, all mortal emotion feeds the Chaos Powers. So even if the Emperor is receiving some kind of power boost, all four gods are too.