I also noticed that knocking a guard out decreases your morality. I feel that the morality system needs a bit of revamp.
Is morality what my character thinks about herself? It can't be that because under the description of the stat it says "Morality attributes affects the attitude of NPCs towards her." so it is solely how the NPCs view your character. If I knock a guard unconscious, my morality should not go down, since that guard shouldn't know who did it.
The thing with the bank may also just be a bug. When you cross the counter door, the guards get aggravated, and your morality drops. This indicates that the guards already know you have entered the restricted area. This still happens even if you knock down both guards near the counter door.