I doubt we see the Passholder Lounge going anywhere. SeaWorld San Diego is keeping the whole Hospitality House building for the their new land. It's being gutted and rebuilt with a new gift shop and restaurant though. I'd suspect if this rapids ride comes, or any ride, then the building will stay put, so the Passholder Lounge could stay.
They already have a well themed rapids ride in San Diego. It would be relatively cheap to rebuild here because all the plans are already drawn up, so I hope this does happen. It seems like a pretty decent rapids ride as well. I just hope they extend the theme of Shark Wreck Reef (Mako area) to this area of the park, which they definitely could. It's another ship from the Wreck Reef that the ship from the queue of Mako is in.
I wonder if they bought a ship and just cut it into pieces for future attractions. Something similar to that ride looks ideal.