You know, technically iw would be assault if you attack another human being first. Even though you the player know that it's a criminal because the NPC is labeled as such, would your character know it just by looking at him? So from that perspective, you are taking on the role of a vigilante and attacking people because they "look suspicious". Maybe they just like hanging out in caves.
So unless they attack you first, it makes sense that you would register an assault.
I think one possible exception to this might be if you were a member of The Blades faction. In which case as a defender of the realm you have the authority to make that decision. Creating a check to see if you are a member of The Blades and to see if your opponent is "on the list" (bandits, mauraders, conjurers, necromancers, etc.) wouls be fairly easy to do. But I'm not sure how to bypass assault flagging part without doing some digging.
You may have to create your own mod, or just let them attack you first.