If that's what The Boss actually wanted (and it was), then there's more of a chance Naked Snake would have complied. Then it would've been choosing loyalty to The Boss anyway.
What did Eva actually get Snake to do that he wouldn't have done otherwise, other than sleep with her so she could take the wrong copy of the Legacy? She had very little control over his emotions or his actions until the very end, and then she botched it anyway.
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