There are lots of ways to setup the interaction of magic-users and the society of a fantasy setting. My take is influenced by the fact that religion and culture play a big part in the forces driving my campaign. The magic-users are not exempted. The key element to remember about the magic-users in a D&D world that despite their power they need time and resources in order to fully realize their potential. Without time to rest and study they will quickly run out of spells and lose what sets them apart from their mundane peers.
Wizards and Society
The magical Orders are a threat to the hierarchy of society since the magic-users bow to neither Patriarch nor Potentate. The Orders are powerful enough to deter rulers from attacking them openly. But the knight's courage and the priest's prayers have supernatural powers of their own, so members of the Orders rarely attack their mundane foes in open warfare. Those who cause undue conflict between the Orders and society are subject to punitive action.
Young magic-users often find the restraints caused by society annoying, and they sometimes skirmish with the powers of the mundane world. Older magic-users, find ways to pursue the arts of magic despite the desires of those who would control or destroy magic-users. They scorn those who do not follow their example. Most magic-users are wary of the outside world. They will go to great lengths to maintain the shaky peace that continues to the present.
Fanatics within the magical Orders and the various Churches have long called for an end to the truce. They desire a final confrontation to destroy each other. So far, voices that are more reasonable have prevailed.
Most magic-users realize that, while they wield great power, they have no defense against miracles. They stay out of the way of the various Churches and not draw attention to themselves. Were they to threaten society, the magic-users feel that they would suffer the fury of the Gods. To complicate matters, many in the Orders are believers and share the faith of many Churches. Typically misunderstanding and/or political intrigue are the base of any conflict between the magic-users and the churches, not moral antipathy.
The various magical Orders realize that aid to the barons and the churches will ease tensions. To this end, they offer their service and knowledge. The Order of Set has gone so far to become part of the triad that governs the Thule Empire.
Aquinas on Torture
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