ok...ive played through the game a couple times and i don't ever remember a reference to Sephiroth controlling Jenova....and honestly, how is a strategy guide proof, unless Square published it then no it doesn't count as proof

In my opinion Jenova is the antagonist because she is the one that almost wiped everyone out, she is the reason sephiroth went insane, the fact that he was injected with jenova cells caused him to believe that she was his mother and he was doing this stuff mainly for her, to fufull what she failed to do...and if you wish to tie in advent children into this (although i wouldnt cause i didnt really like that movie >.>) they constantly talk of "fufilling Mother's mematic (or w/e that word is) legacy" so id say Jenova is in overall control...not sephiroth