The game seems to produce somewhat strange and inconsistent effects when robbing stores. Might be intentional behaviour, but TB had mentioned that he was looking to close "loopholes and exploits" or something to that effect, so I figured this would be something at least worth having a look at.
Basically, when you rob a shop, there are six possible effects: Shopkeeper hostile; Town hostile; Curse; Doom; Alignment Shift Toward Chaotic; Summon Thugs. Depending on how you engage the shopkeeper will give different effects. From the Guidebook:
Action Alignment Curse/Doom Shopkeeper Thugs Villagers
-Teleport PC with unpaid items towards C cursed hostile summoned nonhostile
-Teleport Shoppie towards C unknown hostile summoned unknown
-Stun Ray, Paralyzation, none none hostile none hostile towards shopkeeper
bolt spells, mindcraft
while out of LOS or PC in
-Ventriloquism none none hostile none nonhostile
-Melee shopkeeper towards C curse/doom hostile summoned hostile
-Pick Pockets towards C cursed hostile summoned nonhostile
-Unholy aura none none hostile summoned nonhostile
IMHO: The third and fourth ones should probably be tweaked a bit. I think having a method to rob shops without in any harmful effects, other than the hostile shopkeeper is a bit exploitable. These methods don't even trigger the platinum girdle, apparently.
Regarding the case of having a companion kill the shopkeeper, the act of giving the command should be what affects things, rather than the attack itself - I'm assuming, here, that companions require verbal commands (on that point, can a mute PC give orders to companions and pets?), which would then be heard by the shopkeeper and villagers, and presumably by the gods (cursing, etc) and certainly would affect/reflect your mental bias (alignment).
By the way, can you create traps in shops? If so, what happens if you create an Alarm trap in a position that the shopkeeper might step on?