Actually, from a roleplay standpoint, mission-runners should actually be far more feared and respected than capsuleers who habitually kill their own, because when you kill a capsuleer, it is more or less implicit that all you've done is inconvenienced them - they'll be back. Capsuleers assemble ships and modules in a matter of hours and can obtain all the wealth to replace lost assets in a few minutes, and their expertise and experience is not lost when they die - merely transferred to a new body. When you kill a pirate ship, that's a large investment of time, money and personnel on the part of the organisation in question that's permanently gone. It's actually somewhat rare that a war will permanently destroy a capsuleer organisation, but every time you finish a level IV mission, that's an operation that probably took months of planning and billions of ISK right down the drain.
Besides, since there are more NPC ships than capsuleer vessels, the total human kill count of a mission runner is probably astronomical, whereas since capsuleer ships require a significantly reduced crew, capsuleers who kill other capsuleers probably have a much lower bodycount to their name. If, like me, you serve a faction, you're also most likely performing a much more useful service by completing a mission than by destroying capsuleers.
Yes, I know that's not how it works in out-of-character respect allocation, but remember that in-character, it doesn't work the same way.