If it got to the point where a large segment of their population had converted i don't really see why the monarch himself would not convert. One way I think would rather easily keep at least major segments of Indonesia in the Dharmic fold would be to have Bhakti movement representatives preaching to counteract and complement the Sufi influence. Either way I think there's little way to keep the Majapahit from islamicate influence and styles even if they're kept in greater contact with India due to the cultural dominance of those styles by the 17th century in India. Unless of course, you want to radically prevent Islamic incursions into India which is very difficult.