Witches are a breed of rogue psykers and mystics who have rejected the Imperium and all it stands for, and embraced the fell powers of Chaos. Madmen, lunatics and vile heretics, they are hunted by Inquisitors and destroyed wherever they are found.
The people of the Imperium fear that which is different strange or unusual. Such is the brutal and unforgiving nature of the 41st Millennium that this mindset is a wise survival strategy. Unusual growths, rumors of deviance, supposed magic powers or simple unpopularity are often enough to see a person branded a witch and lynched, burned or worse. The paranoid fear of witches is common throughout the Imperium, and many innocent souls are sacrificed upon the altar of hysteria. Those accused of being witches might be psykers but just as often they are simply a wizened crone ugly misfit or drooling simpleton.
Some cultures add charges of witchcraft to other crimes for reasons political and otherwise. For example, a charismatic sedtionist within the mines of Sepheris Secundus might be tried as a traitor and warlock. His followers might be described as being enchanted or bewitched into acting against their baron. Even on planets with advanced technology such fears still run deep. A dissolute hive world noble might be mind cleansed by his family for treating with the occult or having heretical psychosis. One of the more common tasks of the Inquisition is discovering if a witch has any real connection with the warp or if their crimes are of a more domestic nature. The majority err on the side of guilt just to be sure.
Whilst sorcerers, witches and, to some extent, latent psykers are feared and hated by the common man. Imperial psykers and Astropaths enjoy a different status. Sanctioning imparts a measure of orthodoxy and authority to these psykers marking them as part of the Imperium. After all the Imperial psyker has made the great pilgrimage to Holy Terra and beheld the Emperor's light first hand. Whilst the common man will almost certainly be full of awe and fear at the psyker's presence it is little different to the feeling he might experience when encountering a commissar or an Administratum tax prefect.
That said, Imperial psykers usually take pains to avoid making their abilities too apparent: Mob rule and superstitious rage is never far away particularly when psychic phenomena begin to manifest. Astropaths are usually sequestered far away from the public gaze but even they are conscious that their presence is unsettling for the blunt masses. Most folk will never have heard of a Navigator, let alone seen one for they are a rare breed which is kept closely cloistered and hard at work. On the rare occasions that they deal with human society like other orthodox psykers they choose to hide from plain sight.