I remember at least once (in the Loeb/Lee "Hush" storyline) where Batman was ready to kill the Joker and Gordon approached gun drawn and stopped him and told him he would take Bats in/shoot him if he actually killed the Joker. When Bruce reminds Gordon of what Joker has done to him (crippled his daughter, killed his wife), Gordon says he knows but will not let Batman destroy himself which is what would happen if he killed Joker (paraphrasing here). In Gordon's case, he won't let Batman kill FOR Batman's sake not for the criminal.