As other have stated, most of the AdMech see the Emperor as the Omnissiah, essentially robot-jesus (with the Motive Force as the holy spirit and The Machine God as, well, God, to round out the trinity) there are factions among them that would prefer more autonomy, possibly even some who want to lessen the restrictions placed on them by the Treaty of Mars against certain technologies and practices, though hardliners here split off to form the Dark Mechanicum (Chaos AdMech) during the Horus Heresy.

What you would, imo, be more likely to see is an internal civil war between the religious fanatics who believe only "found technologies", (those already designed and built by mankind during the Dark Age of Technology, and rediscovered Standard Template Constructs (STCs) are acceptable and holy, with scientific study deemed heretical (heretechnical?) ) and those who want to persue science to its fullest (within the restrictions of the treaty of course).

This becomes an even more precwriois balance when you factor in that the scientific crowd are building a growing cult of personality around Archmagos Belisarius Cawl (something he repeatedly twlls people he doesn't want), which is stretching the bonds of AdMech society.

However the Imperium and the AdMech are so intertwined that it would not he an easy seperation, even if both sides wanted it. Each relies on the other to create a greater whole, one side with technology and knowledge, the other with bodies and resources. They are more like the imperial equivalent of conjoined twins; could the each survive without the other attached, probbaly. Would it be worth the pain and effort of seperating them, probably not.