I really like the idea of a legitimately rational sci-fi civilization trying to deal with the WH40K universe, but I feel like your Fic here isn't really "getting" the idea of GrimDark.

Chaos is basically the philosophical equivalent to Entropy. You can fight it, you can hold it back for thousands or even millions of years, but you cannot ever truly defeat it. Preventing people from ever being tempted by Chaos... is not something which should ever happen in a 40K cross-over fic. Manufacturing souls without summoning / creating armies of angry Daemon Primarchs or shredding your own mind is another no-no.

The key thing to remember is that in 40K belief is absolute and facts are mutable. The nature of the Warp is that there is no reality, no space, no time, only infinite power and the countless Daemons and Psykers which fight for it. There is room for science in the Materium, but the Immaterium cannot be analyzed by means which rely on math and logic because those things simply do not exist there.

I would love to see an "Elephant Versus the Whale" kind of story though; the Culture has mastery of the physics of the Materium, the Chaos Gods and the Emperor are lords of the Immaterium, and their conflict ought to be literally epic in scale. Respecting both canons, yadda yadda.

(Also, can Minds/Drones communicate with Machine Spirits? Do they even have Machine Spirits?)