The holy empire was going to summon them regardless because world domination is their goal. Why the goddess(es) can't stop time and talk to the summoned before their arrival to the holy empire and tell them the empires actions are not in line with the goddess wishes does not make sense. As they were able to send him back three years, seems like stopping time for 5 minutes would have been way easier.
Also, the kingdom has flushing, sanitizing toilets; there is no way the kids would side with the holy empire with that option available. MC just needs to invent mayo and soy sauce in this world and the summoned will change sides so quick it will make the pope and princess head spin.