'Loyalty to me' is a very very different question when you think your mentor is supporting someone whose idea of testing a nuclear weapon is to fire it at a lab in his own country. The Boss he thought she was and The Boss she actually was were two different people. And who said that she had to die? The US government, to save their own asses? I seriously doubt that BB would have gone through with it if he knew the full story.
Eva's attempt at control failed when she took the wrong copy, but she still completely manipulated Snake from the start. If she had been a little more competent, it would have been disastrous - but she still played a big role in emotionally crippling BB, anyway.
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Black Turtle did a pretty good job.