Everytime she beat him it was in CQC, the final battle was a gun battle. (With moments of CQC)
Also, he did get better every time they fought in CQC as well.
There could also be the fact that Snake was always resistant to hurting the Boss, and at the end he saw that he there was no other way, it was what she wanted.
Or it could be that he finally found what feelings and emotions to carry in battle, that he wasn't a child anymore like he was at first.
I'm not saying you're wrong, but I think there are a lot of possibilities to explain how Big Boss prevailed aside from her faking it.
http://www.youtube.com/watch?v=COiz4PCVbfk
This is the Boss and Naked Snake's real relationship. 😉