Any of the West (Andaman) side islands will have rough water and poor snorkelling conditions in summer.

If she doesn't want to stay in Malaysia (I was thinking of Redang on the East Coast, or the National Park/Kota Kinabalu area in Sabah), then I'd say either the Samui group of islands in Thailand or the Phillipines--though I'm not knowledgeable on weather and water conditions in the Phils at that time. Bali is really not a beach or great snorkelling destination (for diving, it's got a few things and it's a great cultural destination). You might consider Bunaken off Manado in Indonesia--I think Air Asia has direct flights there from KUL. Most anywhere else in Indonesia with decent snorkelling is not doable logistically to fit into your tight schedule. Any cheap packages from Malaysia out to the Maldives?