We should focus on Indonesia, because it's easier for Indonesia to culturally influence Malaysia than the other way round.
1)Keeping the Hindu Majapahit Empire and minimize the influences of the Islamist city-states of north Java?
2)The Dutch replaced "Ethnic Policy" with "Missionary Policy", and make Christinization a part of their Culture.
3)IOTL, One Indian soldier under Sir Thomas Stanford Raffles tried to convert a Javanese king back to Hinduism, and (according to Raffles) almost succeeded, because Java still had strong Hindu cultural background.
ITTL, If the British stayed longer with their Hindu mercenaries, and forcibly got rid of the Arab-descended Sheikh-class, they would have stopped the (then-superficial) Islamization and convert Java back to Hinduism.
Later on, the Javanese decide that Hinduism is a part of their national identity, and radiate Hinduism to entire Indonesia.