but only if the clean ship is of a faction in the local system correct? otherwise its just a crime/murder ding against the controlling faction correct?
that is if a clean ship from a faction not in the local system is attacked/killed that faction would not suffer an influence hit or will it?
As far as I can tell if you kill a ship from a faction external to the current system (i.e. it has no faction locally) it counts towards civil unrest to the local dominant faction. It also makes you wanted in both local and that other factions territory, if they hold any, and lowers rep accordingly too.
External faction ships are only useful when luring sec ships to fight anyway. In low population / spread out systems it takes a long time (if at all) to see the correct faction type. Thus, its easier to interdict passers by to get security to pop up.
OT:
If you want to make murder less effective but still keep it fun, up the cost of hot modules and bounties. I had to burn a Corvette the other day and pick a lot of body parts out of my ships modules, and it was quite expensive (to pay my dues, I'd have to fork out half my total credit balance-fat chance!). Now I use smaller, less expensive ships that are slower to rack up kills (and are more fun at the same time). BGS murder benefits are front loaded in that you can kill quite happily but eventually you have to pay. If the 'pay' part came much earlier (and the ceiling for ATR was lower) you might put even the most hardened BGS sculptors from using large farming vehicles and swap to smaller ones, or at least make it so burn ships can't use engineering (as A and B grade modules are expensive).