I don't see why anyone should object to the Pakistanis cleaning up their ranks. Why is this bad?
Because this is a sign of how bad the Islamist tendencies in Pakistan's army have metastasized into. If you're a student of history, you'll see parallels between this and the slow Islamization of the Iranian armed forces before the Shah was overthrown.
I don't think you'll find too many people surprised to hear about this. What is encouraging is the steps being taken to root out this problem. Pakistan has come a long way in the past three years, but there are obviously still many problems.