Is that not basically the theme of Snake Eater? "Scene"?
Your closest allies can become your greatest enemies depending on arbitrary circumstance.
People like to complain that the Patriots being the MGS3 cast was a bad twist shoehorned into MGS4, but I think it was pretty clearly established from the start.
The reason it feels shoehorned is that the motivations don't really make sense and aren't really explained. Had it been done better I would agree with you though.