If the Adeptus Astartes are starting in the southeast corner of the map, then the walls on the east side of the Adeptus Sororitas Mission don't actually block any shots. Taking hits from the Exocrine, gargoyles,Termagants through it, and i can shoot through it as well.

Yeah, it's still happening in my present campaign as well. Has to be a bug. Wish they would fix it soon, as the mission is tough enough trying to save as many of the Sisters as it is. Hopefully this will be addressed in a patch in the very near future. It's not game breaking, but really does ruin the mission strategy.