Remember he is alleged to have committed a sexual assaulted on 16 year old girl and nothing was done - he then he went on to assault another girl.
Updated stories do say the Vatican said he should be defrocked but such a decision under canon law is up to the Bishop. I don’t know why the Bishop did not take further action. Especially in light of charges being filed.
However since NYT is notorious for half facts I well reserve judgment until the full facts come out.