Thanks for your comment virazdan.

I believe it was less due to ahimsa and lack of resistance by the Buddhist kingdoms, and more due to structural matters.

The Islamic sultanates, once established, were based on the coasts of Indonesia — for reasons described above.

This had the additional effect of giving them a “better hand” than the Hindu-Buddhist kingdoms of the interior. With better access and control of markets — they were able to better finance their endeavours as well as re-supply.

You’re correct that many of the fleeing Hindu nobility were thought to re-group in Bali. While it is possible that Bali would eventually fall to the sultanates — even the Dutch themselves did not fully subdue the island until the early 20th century.