I too see that as a problem. But I think the idea of a "peasant revolt" in general is a bit strange. Unlike today the ruling class of the day consisted of professional warriors who trained all their life for war. Revolting against such a class as a commoner who has neither the experience nor the equipment to fight on the same level would be suicide. Also culturally commoners generally knew their place. The church cemented the idea of the classes being gods will. Thus peasant revolts were quite rare during the middle ages. Also why should the town revolt against their lord? What benefit would they have for doing so? The villages won't resurrect themselves when the lord is gone.
"Rare" is a relative statement but lower class revolts did happen. I'm not expert and here is a list of medieval revolts that were largely lower class in character from the top of my head. I'm sure an actual historian would know a lot more:
Europe:
Peasant Revolt in England
Hussites in Czech
Peasants War in Germany
Muslim World:
Mamluks were a class of slave soldiers who rose up to control a sultanate
Japan:
Ikko Ikki movement
China:
An Lushan Rebellion
To say it was "suicide" is also not always correct. Sure, they lost a lot, but they won too. The Hussites won every battle and were only defeated through political maneuvering - and even in defeat some of their demands were met. Ikko ikki defeated many samurai armies and controlled areas of Japan for over a hundred years. Mamluks gained political power and overthrew the previous dynasties.
I assume by "the church" you mean the Catholic Church. Just a reminder that the Cathoic Church only influenced a small area of the world in the middle ages. If we assume a 1 to 1 correspondence with the factions in the game and real world examples only 2 factions would be influenced by the Catholic Church - Battanians and Vlandia. Khuzaits are based of nomadic groups and would be animist, nestorian christanity, or tengrisim. Sturgia are based of the Rus and would follow Russian Orthodox. Empire are based of the Byzantines and would follow Greek Orthodox. Aserai would be Muslim. So what the church teaches wouldn't be relevant for everyone, and was only relevant for a small part of the world in actual history.