Let's go back to the whole "cloning the God-Emperor of Mankind" idea for a moment. Take Star Wars cloning tech: I think we've got sufficient evidence to conclude that it functions perfectly insofar as that it creates exact genetic duplicates of the original donor, but the issue is whether it would also function in such a way as to transfer the GEoM's pskyer ability/status as a living god to the clones. If so, any Imperium v. Empire scenario would end pretty much the moment a reasonably sound of mind Imperial got their hands on SW cloning tech and... Okay, it would be game over after several months/years/decades of travel, when it got back to Terra. I think the thought process there could probably follow this pattern:
[Assumption]: Cloning duplicates the body.
[Knowledge]: GEoM's body is failing, soul is intact.
[Knowledge]: GEoM is, as indicated by the name, a god.
[Assumption]: ∴ if a duplicate of the body of the GEoM were to exist, he could transfer himself to it.
(Note that this may take the form of the 'pull the plug' scenario with that splinter section that wants to go through with it.)
Once they clone the GEoM, assuming his status as a god is preserved, everything is irrelevant. You've got a GEoM with no experience (given that the Jango clones had to be taught everything during their development cycle rather than inheriting his knowledge), who will be raised by the bloody (in more than one sense, hah) Imperium. Best case scenario for everyone involved is that his natural talents and intelligence guide the clone onto the same path as his "father".
The worst-case scenario is that you have a God-Emperor of Mankind who completely buys into the superstitions and pathological hatreds of the Imperium, with the ability to clone himself endlessly. Every enemy of the Imperium would be overrun by a virtual tide of power-armored God-Emperor clones. It would turn the Imperium into the gorram 'Nids!