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Would an alternative IoM ever work in the 40k universe? Sort of like atheists, they wouldn't be zealots for the Emperor or worship him as a God, but rather fight for their colonies and to survive. Not taking orders from Terra.

Splintering from overly religious SoB to the practical IG.

That already happened; it is called mechwarrior or votoms or starcraft. Actually it is exactly starcraft.

And, since the Imperium does not exist or include real people, maybe it does not matter whether it operates the way you think it should. You could extract some kind of literary value from mysticism, which may be the entire point of the setting. If not, I still suggeest starccraft.

"Practical" IG? I must have missed something.

But yeah, I'd say that the mysticism/superstition, religion and loss of knowledge are unique hallmarks of 40k's humanity. Take that away and you have ... yet another sci-fi setting with humans in bulky armour and laser rifles. Don't get me wrong, that doesn't have to be bad, but I do not see what else the IoM should have to offer that sets it apart from stuff that already exists in another franchise.

Every once and a while, a planet or several planets get this kind of idea in their heads. But then an Inquisitor comes by for a chat and everything is put to rights, praise the Golden Throne.

The worship of the Emperor is the only thing that keeps the Imperium together. Its the one common thread its diverse people have.

Without it, the Imperium would have been destroyed long ago and its all thats keeping it together now.

I'm not sure what you mean. Are you talking about a replacement/retcon of the entire Imperium? If so, I don't like the idea, as it pretty much undoes what makes 40k unique. The Dark Ages Catholic flavor of the Imperium is the defining characteristic of the setting.

On the other hand, if you're wondering whether such a society could survive in the 40k universe, the answer is yes. During the Great Crusade the Imperium encountered lots of human civilizations that were secular, which were fairly easily integrated as the Imperium was much like that at the time. These states had survived the Dark Age of Technology just fine (the ones that didn't get perverted by chaos, at least), so long term survival of such a society is possible as long as they can deal with the threat of rogue psykers. Now in the current state of the setting, such a society is either going to be so far-flung as to have no contact with the Imperium, or if they are a former Imperial possession the lifespan of the state is going to be fairly short before the Imperium comes to reclaim its territory. Of course, fairly short is probably a few centuries, so there's plenty of time for it to become a player in sector politics.