Mr Norie Usman, is the former right-hand man of a leader of the infamous Ampatuan clan.
Since the author used the word "which", he is referring to the whole Ampatuanclan (not Mr. Usman) when he says that it (the Amputan clan) was a close ally of Arroyo's (clan).
If the author had used the word "who", he would be saying that the leader of the Amputan clan was a close ally of the man "Arroyo".
Tan Elaine, only you know the context in which the sentence was written. Given the information I have supplied, what do you think it means?
Student or Learner