Ganondorf may not want kill him until he has control of the tower. He'll probably wait till the very last moment even if he got Demise's powers.

Especially if we can have that awesome thing of them accessing the control room (I can dream, right?). I mean, they would have no idea what to do and Ruana would push the kill button sooner or latter, BUT-

And I can imagine Fado or some Links pushing buttons at random and worsening the situation.