However, is this simply the way the current government works (with the High Lords speaking with the Emperor's authority)? Would the Emperor himself have had less qualms with occassionally allying with, say the Eldar?
In that specific regard, are there recorded instances on the Emperor having any sort of interaction with the Eldar?
This quote is not directly related, but it seems to indicate that the Imperium would have been a normal, peachy sort of place to live in, had the Emperor not ascended to the Golden Throne.
It's from en.wikipedia.org/wiki/Word_BearersOne of the Great Crusade's major objectives was to liberate humanity from the shackles of religion and thus the Emperor personally reprimanded Lorgar, informing him that his task was to free human worlds from alien oppression, not re-enslave them under a new tyranny.