Alright there's a little too much speculation going on here for my likings. I'll clear some things up for you guys:
Oregons herd consists of three different subspecies. Their new breeding bull Samson is a Sri Lankan x Indian cross. All the animals living at the zoo that were born there (rose-tu, shine, lily, and samudra) are all pure Indians. Chendra is their bornean. They don't have any "Malaysian" elephants. Additionally, Oregon was actually the first zoo in the US to produce a third generation captive bred elephant. As a matter of fact, all of the animals at Oregon bar chendra are second or third generation captive bred.
As for EEHV, oregon is one of the few zoo's unaffected by it in the past 20+ years. The past three calves born there (rose-tu in '94, and then her calves samudra and lily, born in '08 and '13 respectiely, are all alive and well, and not affected by herpes. The past three deaths at the facility have all been mature bulls 30+ years old, Packy for TB and Tusko and Rama for foot issues.
As for management, they are protect contact as per AZA requierments, however this was a recent change only coming into play in the past few years, and like several others (including the smithsonian, houston, and rosamond gifford), they are rather lax with what all entails protected contact at times. Technically the pool sessions are protected contact, as the keepers are not sharing space with the elephants, the barrier being the deep pool. It's no different than working an animal through a fence made of wire strung two feet apart, that many exhibits have. It's by definition "protected contact", but not really. True PC with eles is behind walls that their trunks can't fit through.