Nah, its just a narrative inconsistency.
They should lock the church before you manage to deal with other threats - henchmen, or if you go into the church directly they should remove the henchmen from the areas outside. And this the players would loose the loot and xp from them.
Since that will make the mass market cry and stomp their little feet, the devs have decided to implement the old "have cake and eat it too" trick.
Having the church be magically locked until you see the scene in the cultist lab would probably solve that, and I don't really see a major downside to locking the church like that. Some people might complain if the church door is locked and unbreakable, but too bad.
