Sounds like a slightly better outcome than OTL.
For East Timor: probably. Basically there was a 3-way split among the Timorese between staying with Portugal, joining Indonesia or going it alone. Fretelin, the independence movement, was considered too Marxist by the west and Suharto was an ally of the west, so everyone turned a blind eye to the Indonesian intervention--a fact that caused a lot of subsequent guilt on the part of Australia and Portugal.
Here, if the Indonesians still try invading--and a lot of the logic, including trying to balance the restive Muslim population by adding more Christians, still applies--Australia won't hesitate to intervene, even under a Labor government. Got to burnish those anti-communist credentials and such. Also, given the fate of Papua and the death of the white Australia policy, just directly adding East Timor to Australia may even be a plebiscite option, and if they vote to join Australia Indonesia's going to have a hard time justifying their invasion to their Chinese backers, who may not want open war with the west so soon after Vietnam.
As for Indonesia proper: one of the secrets to Suharto's success, apart from the brutality and ruthlessness that generally attends military dictatorship, was his ability to keep Nahdlatul Ulama, Indonesia's largest Muslim organization and a bunch of raging moderates (or at least anti-fundamentalists) by global standards, on his side. This allowed him the flexibility to crush both the communists and the Daral Islam resistance movement, which was, as far as I can tell, proto-Islamist. NU was very sympathetic to the pancasila ideology, which explicitly supports theism, though not Islam per sey, as a pillar of the nation, and creates Duch/Belgian-style institutionalized support for religion.
So does the new Communist-influenced coalition keep the pancasila balance or not? Because if not, they're going to have some very serious problems. And I can't see how they do keep it under the influence of Madame Mao.
So TL;DR: Indonesia could very easily turn into a hot mess.
[I'm doing work on Indonesian Islam for my dissertation so it's a particular interest of mine].