Keep in mind, that Merlino was in jail at the time. Ligambi was acting boss, whom at one point was a loyal Scarfo soldier. The same guys Merlino came up around, Scarfo Jr was also exposed to, they all being friends at one point. The cookie just crumbled the way it did, it was business. I don't find it unlikely that with Merlino out of the picture, some of his most loyal guys would've went along with the opposition, that being Scarfo Jr. It's happened to greater mob bosses, see Vito Rizzuto. Now we're learning that Scarfo Jr was close to more than one NY mob family, and was still thriving in some capacity off of his fathers connections. With some Gambino/Columbo/Lucchese crews, including his own, backing him, and had he gotten the okay, Scarfo Jr. would've never had to step a foot in Philadelphia until everything was all said and done. He could've supervised everything from New Jersey.

And also as we know, a lot of connected people, even in Philadelphia weren't happy with the Merlino administration and found Philadelphia LCN to be a mess. There's really no telling whom in Philadelphia would've sided with Jr.