Yes, conquest was very limited. The first city didn’t appear until roughly 4,000 BCE and the first empire, considered the Akkadian Empire, didn’t appear until 2,300 BCE. Egypt was unified in 3,100 BCE, but wasn’t considered an empire because it was a collection of villages stretching up the Nile. The first city in Egypt was Memphis, founded to better administrate the territory rather than for agriculture like in Mesopotamia.
Even once the bronze age started in roughly 3,000 BCE, religion was used as a tool to create stability and promote “sameness.” Each city-state typically had a patron deity they worshipped and upon conquest the conquers would say “Hey that goddess you worship sounds a lot like our goddess of fertility, they must be the same god.” Then that instills the idea that these two ethnically and culturally different people are actually “similar” and integrates them into the empire, preventing them from rebelling.
The first religion to only promote belief in one god was Judaism. The only reason the Romans cracked down on Christians, who they originally saw as a sect of Judaism, was their practice of meeting in secret and general disrespect for the rituals of the Roman Empire. The Romans believed that their entire empire hinged on everybody practicing the proper rituals, which Christians refused to observe. The Romans practiced Hellenistic Paganism and believed there was a god governing every aspect of life. The Pantheon in Rome has a statue for every god they could think of and even the unknown god, so if they missed a god, that statue served as a catchall. As you can see, this is pretty generally applicable and just about anyone could worship any of these gods under a different name serving the same purpose.
I agree, anything that would’ve been possible at this time should definitely make its way into the game to allow for historical accuracy. It would definitely be interesting to see a village perhaps not have a standing guard or weapons and then a more aggressive village seeing a good opportunity for loot and slaves.