Even though the war was essentially over once Phil got clipped, Tony's crew had been brought down to nothing. He would have only had a few good guys to work with after that. Patsy probably would've ended up number 2 because of Meadow and his son, and if Silvio came out of the coma he'd go right back to what he does best.

Side Note: Does anyone else find it interesting how often Tony puts guys in their positions simply because of family matters? (Chris Bobby and Patsy are the 3 I'm thinking of). Tony respected guys like Vito and Carlo more than these 3 yet he still pampered them because they were family.