Actually I think you hit the nail on the head right here!
I think a good analogy would be like God, Angels, & Humanity to the Emperor, Astartes, and Humanity. God created the angels to watch over humanity and protect them not to rule over them.
I like this. Because we also have the Fallen Angels in the Chaos Marines.
Another answer imo could have something to do with the nature of the chapters. Given their autonomous nature and independant status, I doubt any single representitive could properly speak for the astartes as a whole. Some chapters are just too remote, secretive or untrusting to share any semblance of agenda with each other.
Added to the fact that none of them have any desire to be controlled by the adepts of Terra.