What the Phillies did was different than burying worthy prospects.
Ruf - never was a top prospect. Played well when Howard was hurt one year but not really better than Howard. Plus he had failed in AAA that year. Look at the two year by year and you will see the point. In 2013 Howard had a 784 OPS and Ruf 806. There were reasons to think Howard might improve if he stayed healthy and reasons to think Ruf was not real (his OPS in AAA that year was 749 so his full OPS was worse than Howard). In 2014 both got worse which continued in the future. Ruf never earned anything because he never outplayed Howard and was correctly seen as a non-prospect.
Utley - Not buried. They incorrectly did not think his defense was good enough. This is also ancient history so it applies less to worries here. The 3B move is not defensible though I think the motivation was different than playing the veteran. It was not believing the prospect could play 2B.
Brown - I agree they should have let him play and not acquired Pence. But they were fighting for a World Series and Brown was not lighting it up. I did not think they needed to get Pence and overpay, but Pence was clearly the better player at that point. Again this is not burying a good prospect playing well. It was delaying a good prospect to compete for a pennant with a better player.
Hernandez - Was not buried by Utley. He was not considered a top prospect and Utley was always clearly better when Utley was with us.
Atherr I guess could be considered a B level prospect, but we still don't have many examples of young players that play well and then get buried. Werth also boosts my case. Werth always had a platoon role and when he outplayed Jenkins he got the job outright. Which may be happening with Altherr.
Sometimes we invent or inflate behavior from the Phillies management that is not there. Unfortunately we have not had enough good young prospects for a huge sample size, but it really seems the Phillies biggest error was sometimes trading for better players when they were competing for a pennant. We do seem to have integrated Franco and Herrera and Rupp into the lineup at about the right speed and they certainly gave Joseph a chance last year to take the job from Howard by the end of the year. Yes they played the veteran a little too much for sentimentality, but Joseph had zero prospect status starting the year and ended up with a half season of playing time with the first month in the minors. Which again is not burying a prospect that played well.