Option A, you kill me right here and now. Apparently I've made that very easy for you. You can kill me, no witnesses and then spend the next few weeks or months tracking down Jesse Pinkman and you kill him too. A pointless exercise it seems to me but that is Option A. 

I continue cooking, you and I both forget about Pinkman. We forget this ever happened. We consider this a lone hiccup in an otherwise long and fruitful business arrangement. I prefer Option B. 

He'll live. I asked to see you in order to... clear the air. There are uh, some... issues that could cause a misunderstanding between us and I think it's in our best interest to lay the cards on the table. My brother-in-law, moments before he was attacked, someone called to warn him. I believe that same person was protecting me. 

Those two men, the assassins. I believe I was their prime target, but that somehow they were steered away from me to my brother-in-law. Because of this 'intervention' I am alive. And yet, I think that this person was playing a much deeper game. He made that phone call because he wanted a shootout not a silent assassination.