The whale shark was a complete blessing from above! The DM was as blown away as we were...he had never seen one in the straight before, had only heard rumours.I'm going to see whether I can convince her to do the open water in Bali.
Your pictures of Lembeh look amazing! See you even spotted a whale shark, when did you go?
Regarding the other places: I know my wife does want to check the typical bounty / white beach vibe and just walk into the sea easily. I'm going to check out the resorts and place mentioned again.
As for the picture perfect beaches...Murex does have a beautiful beach as does Blue Bay Divers. In fact Blue Bay has just opened up a new resort in N Gorontalo called Saronde Island Resort, which looks pretty and ticks the white sand beach box for sure.
My wife hated snorkeling but fell in love with diving. So if your missus already enjoys snorkeling then it shouldn't be too much of step to get her underwater... Good luck!