If you hadn't killed covenant you would have found some guy in there (forget his name) looking for info about a missing caravan and in particular one npc, he recruits you to do the quest, once you find out where to look as you go to leave you'll have a speech check with one of the named npcs in covenant who will, if successful, tell you where to go and that he'll let the guards know to expect you. I got there and the guards were hostile, long story short, they all died, talked to the doctor she told me I had ruined everything and that she wouldn't beg for her life. Left her in there surrounded by corpses, freed the prisoner went off and did something else, happened by chance to be wandering past covenant a few days later and they got a bit pissy, hence the arty grenade.
Got a settlement with a nice pre made wall around it though I suppose