I am trying to do a setting based off of Warhammer 40k, but less grim dark and more 'realistic'. In this game, a brutal theocracy rules humanity and protects it from daemon, alien, etc. There's what they call a Geneseed that comes from the settings equivalent of demigods. It is only compatible with boys and turns them into super soldiers. These special children would represent about 10% of humanity and is completely incompatible with girls.
What I was thinking was that instead of the geneseed only working with men, it would simply affect the sexes differently. Boys get the physical benefits (enhanced musculature, etc) and women get access to divine power that come from the gods These abilities would be based on ritualized magic and would be very powerful but complex and time consuming. They would take hours to activate and some may take days to prepare.
In this setting, these special individuals would rule over humanity. Men would be seen as protectors and defenders, who mould and shape it to suit the emperors vision. Women would be seen as its guiders, who have access to the gods and would be seen as sacred. They would dominate the faith and serve as keepers of religious law, as some sort of high council or supreme court.
My question is can a setting like this work as a story or is it too implausible? What pitfalls should I watch out for and avoid? What elements of it should I expand on?