You're forgetting all about Sandberg, not that I blame you! But if we play this fantasy out Charlie doesn't even get fired when he does and Mackanin is probably never the manager (maybe Sandberg still is, to start the rebuild, or it's someone else entirely).
The big variable in 2012-2013 probably would have been the Phillies' ability to add another starting pitcher as Halladay faded, though even in my alternate timeline they probably still let Papelbon eat up too much cap. But the 2012 team still won 81 games with negative WAR from Howard, Dom Brown, Ty Wigginton and Polanco (was his defense gone or was he actually that bad offensively?). It wouldn't have taken that much to win 86 games (though the second wild card that year did win 88).
What I really think about those years is that they should have busted the luxury tax. Kept Pence, re-signed Vic, found another pitcher better than Burnett. Or started the rebuild, of course.