From: KamikazePotato | #121
Do you really think BB would have killed The Boss if he had known the full truth? Would he have gotten close to EVA if he knew she was a Chinese agent? Deceit is control.
The Boss poses the question to Snake right there at the very, very end: What is it going to be: Loyalty to the mission, or loyalty to me? It's hard to say what Snake would have done in that situation even if he knew what The Boss's mission really was, but regardless of whether he knew it, she had to die anyway.
But what control did Eva actually exercise over Snake? She stole the wrong copy of the Philosopher's Legacy and she didn't shoot him because she promised The Boss she wouldn't, big deal.
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