I personally, would rather believe Tony didn't get whacked.... The only precedent for it would be Butch backstabbing Tony (which is totally plausible) but I get the feeling Butch would have been satisfied with Phil dead, Little Carmine would've been a level-headed mediator and I don't think anybody wants to be at War for too long.
Also getting rid of Tony would pretty much make them non-grata as a Family (coupled with Carlo flipping), they would literally be a "glorified crew".

Either way the Soprano Family would never be the same after that War. The prospects for the top spot would be laughable, Paulie (even though by this point he is alittle older) I just can't see him being good business-wise, probably wouldn't have problems within the Family, Silvio (just gonna assume he was out the picture) but at best would be a semi-retired advisor but as Giacomo stated, they would be going in a Carlo case along with Patsy. So there's Cagey Albert Barese, constant law issue Larry Barese, too young Benny and Walden and a freshly released Joe Beppy Sasso..... Doesn't Sound to promising for Jersey.