The impression this Baptist has is that the Vatican is cracking down on non-Catholic nuns. I may have theological differences with the Catholic Church, but I can understand why they would want their nuns to be...well, believers!
Why would they want nuns who rejected God?
The problem really goes back to what happened after Vatican II. Many convents were decimated because some used Vatican II as a reason to "breath new spirit into the Church." Problem is some people had no idea what spirit they were letting in.
What the Vatican is doing is correct. What you are hearing from Gramick and the author of the Time article are really some of the last gasps of that spirit as it is being ripped out of the Church.