Right now it gets rid of every religion except the current state religion, which is almost never what you want to do because by the time you get access to inquisitors you have 2 or 3 religions you have founded yourself and have temples & monasteries for all of them. You only want to get rid of your enemies' religions to prevent them from having sight & espionage bonuses against you.
Ideally the inquisitor should have a separate mission button for each religion, and when you remove a religion from a city a number of refugee units should spawn on the city depending on the city's size & how many of the purged religion's buildings were present in the city. The refugees should spawn under control of whichever civ has the purged religion's holy city & has that state religion, or failing that the closest civ with the purged religion as the state religion. Refugees would work like immigrants that can pass through enemy territory. They could even have a mission button to buy a transport ship while inside a coastal city so they could evacuate over water. If you were really mean, you could send bandits out to kill them, but they would have a high evasion score & 2 movement so in a well developed civ they would be able to hop from city to city to stay safe until the reached the coast or the border.
