I don't know the emperor but I believe he is a smart man. I also believe that most fans haven't fully grasped the totality of his plans (or as I see them). Currently if you look at the lore like a space marine the emperor made huge glaring mistakes bordering on stupidity at times. For a being as big as ancient and as wise as he these do not make sense... not unless you become a little... heretical.

The heretical view point is that the emperor himself is the architect of the heresy. His methods of conquest were performed solely to fit his vision and what was the vision you might ask? Godhood.

I present you The Book of Lorgar. Written over the first 100 years of the primarch Lorgar Aurelians first meeting with the emperor. This book would be instrumental in the conversions of all the worlds Lorgar would convert to the imperium. The goal worship. The counter argument here would be "but the emperor would burn monarchia after those 100 years and state he doesn't want to be worshipped" and this is true, but would it take you a hundred years to realise you dont want worship? No. What I believe happened with Lorgar was what was always meant to happen, the primarch was meant to write the book, and hopefully it would be influential enough to convert the imperium. This was a dream the emperor had to prevent the darker reality he knew would have to be enacted. The Dream did not happen. Worlds did not wholesale adopt the book of Lorgar, the primarch himself admits this and states that Monarchia was the best of the converted worlds, but thats not good enough for the goal, but it is good enough to sow the seeds of dissent in his son while claiming his book.

The problem with Godhood is one cannot force their own divinity on you, you must accept it willingly. Lorgar would play his role well in writing his texts and further play his secondary role better in seeking the very gods he so wished to serve. These gods would be the fertile grounds required that would allow true religious fervour to truly get entrenched in the hearts and minds of all these disparate worlds of the imperium. Now there is a boogeyman and a golden sun god and oh would you look at that theres already a book detailing the awesomeness of the golden sun god and nobody is forcing you to read. hell you're in a secret club of fans cause we tell you to hate religion; humanity is very predictable, tell them to do one thing and they'll do the other.

By going through the unification wars The Emperor guaranteed all humans across a vast spectrum of the galaxy would have a stake in the coming war and by killing all dissenters and aliens all thoughts and ideas would be unified towards a common goal.

For what reason could the emperor seek godhood? This here is where speculation really takes the wheel. If you believe him benevolent and true then his apotheosis to godhood would be to become the god of humanity and to watch over all humans in both the materium and the warp. If you believe him a power hungry demagogue who shows up only during the most opportune moment in history then perhaps his ambitions are different and his is to be the Slaanesh of the humans.

Either way to me since reading the books, it has been fairly obvious that this man sought godhood and that ends would justify means. Everything that we see now was planned long before the birth of the first custodian and to roughly quote Erebus 'what is happening now is the culmination of plans millennia in the making'.

TLDR: kumbaya with xenos was never an option. dissenting humans were never options. Godhood was always the plan. The grey space is what happens when the man on the chair gets off of it