So, he's to suspend his God given ability to discern and just let someone above him lead him into the wrong path?
Father Frank has helped many people, like the family of Baby Joseph, who would have died in a Canadian hospital instead of their family's home. How many children are alive today because of Father Frank's efforts?
You seem to understand this in a way that is completely incorrect.
On the day that he was ordained, Fr. Pavone made a vow of obedience to his bishop and to his bishop's successors. Therefore, he is to obey his bishop in all matters other than an extreme case (such as if his bishop were to order him to do something sinful).
That doesn't mean that Fr. Pavone can't make his case to continue working with PFL (and I would guess that he did), but once the bishop has made his decision, it is Fr. Pavone's role to obey it. In a case such as this one, his bishop will not lead him into the "wrong path." It may not be the best thing for for Fr. Pavone, or for the Pro-Life movement; it may even be that the bishop is not of good will (I'm not suggesting this, but it's possible) -- even so, the best path that Fr. Pavone can take for the good of his own soul is to obey.
No prudential argument -- no 'look at how much good was done' type argument -- can trump this.