If Ryan Howard is OK with his role, nobody else should mind
The reality is the Phillies haven't had very much to gain by parting with Ryan Howard, which is why the future Wall of Fame first baseman is still around. If they could have given him away for a career minor leaguer, they would have done it. The reality is that Howard in his current incarnation simply doesn't merit a roster spot for any team that might have a need at first base or designated hitter. If the Phillies had gotten any indication that keeping Howard around would be bad for the team, I don't think they would have kept him around this long. The reality is, Howard has been a model teammate, and he hasn't said a word about his ever diminishing role. Since the start of the season, the Phillies have parted ways with Cedric Hunter, Emmanuel Burriss, Darin Ruf and David Lough, and as bad as Howard has been, he wasn't as bad as any of those four, at least according to the numbers.
This is Howard's fifth season season since he ruptured his Achilles against the Cardinals. During that stretch, he's hitting .225/.292/.414 (.706 OPS) with 575 strikeouts, 154 walks and 79 home runs in 1,921 plate appearances.
Howard hasn't been even close to adequate against right-handed pitching, hitting .154/.222/.338 with 48 strikeouts in 130 at-bats. It goes without saying, that's really, really bad. The question is no longer whether Howard should be playing regularly. It's whether he is even the Phillies' best option in a situation that calls for a left-handed bat, either as a pinch-hitter or as a sub who can give Joseph a periodic blow. With Jimmy Paredes and Cody Asche now in the fold, and with Andres Blanco continuing to perform well off the bench, Howard is, at best, the last option on the bench (back-up catcher notwithstanding).
In a strict meritocracy, you can certainly make an argument that Howard is the best available option for that specific role. If they had a better one, I would be mildly surprised if they refused to exercise it simply to avoid cutting Howard. Up until now, it hasn't made sense to cut Howard, because doing so would be cutting him just for the sake of cutting him. The issue that the bottle-throwing incident raises is whether keeping Howard around might end up doing more harm than good as far as his legacy is concerned. From the Phillies perspective, as long as Howard is OK with his role — and by all accounts he's been a positive influence in the dugout as well as the clubhouse — then why force something that doesn't need to be forced?