If you're doing both sides you won't want to do the kunar quest anyway. I buy everything I need from him before I kill him anyway.

variol - you can actually do all three things. first, contact kunar with the secret phrase, then kill him, then turn him in to the sgt. you get all the experience and you can still complete the alliance.

however, keeping kunar alive until you turn him in can be good for his stuff. for example, only kunar and crock carry impaling stones. and i really hate crock ;)