He could do it wearing Glenn's face. Done.
Alternatively, out Rufus as Sarruff, creating an instant double civil war are hardline Wutai and Shinra loyalists are massively betrayed and turn on their masters.
One of the things that isn't very clear is why the Wutai war hasn't already kicked off.
Hawks:
Prez, Heidegger, Scarlet, Rufus (until his father's death), Shinra Resistance Committee (or else they wouldn't be the Shinra Resistance Committee), Sephiroth via Glenn.
Doves:
Reeve, Palmer, Godo. The first two have no power and Godo was overthrown specifically because he was a Dove. Rufus might secretly be a dove now that his father is dead but can't openly admit that.
Hojo is neutral, not because he's a pacifist but because he outright doesn't care.
All of the powerful people are hawks who have been spending their screentime doing false flag operations. In addition, Sonon and Yuffie outright broke into Shinra HQ and slaughtered a bunch of Shinra staff, and Yuffie tried to assassinate Rufus on live TV!
How did a peace treaty get signed in the first place with these people in charge, and why has President Shinra not already kicked off the war years ago if he wants it so badly? He can't openly break the terms, maybe, but he could just fabricate an excuse if he wanted, which is something Shinra does all the time (see: Sector 7)
This wouldn't matter so much, but a big hook into part 3 is whether/how the Wutai war kicks off, and Sephiroth concocting elaborate schemes to bring it about, but why does he need to when everyone with power already wants a war anyway, and has for years? The party will have to play some kind of role in this, but it's difficult to do that if the setup doesn't make sense to begin with.
The other thing is, Rufus can see whispers. They wouldn't have written that if it never comes up again, so he must have some kind of role in the whisper plot later? Rufus and Sephiroth agree that the Wutai war is a pointless distraction, but it's a pointless distraction that Sephiroth goes to significant effort to bring about even though he also doesn't care about it, and spends so much time screwing with specifically Rufus' head in the process, even at the expense of kicking off the war?. The story is clashing with itself, because Wutai war is a pointless distraction that is also really important, and somehow hasn't happened yet even though everyone with power already wanted it.
There's been so much time spent setting this up narratively, are they going to spend a big chunk of part 3 on something we have already been told doesn't really matter? Or are they going to drop the hook like they did the Remake Whispers? Tough thing to write either way.