You can't blame the Dutch for it. The Dutch actualy wanted such a thing as an independent Moluccas and West New Guinea; they were forced by the international community and the USA to hand it all over to Indonesia.
Actually no. The Dutch wanted a commonwealth of quasi-independent states with err... "closer ties" with the Netherlands.
Here you can see the Dutch proposals in
1945 and
1946. The van Mook idea of a federation IMHO is a great one. The top official of the NICA, HJ van Mook, Charles van der Plas, and the Javanese Abdul Kadir were actually sympathetic of Indonesian independence, however circumstances, that being the republican revolution, driven the federal idea into nothing more than a divide and conquer strategy.
Now, Christians were not submerged in a sea of Muslims. The second prime minister of Indonesia was Christian, so were many of the new nation's generals. The nationalists actually fought hard to make sure the newborn republic did not become an Islamic one. Suppression against Christians is actually a new phenomenon here, and not one that's going to stay. I have to stress that the Indonesian nationalist movement is not an Islamic one. We actually had to put down revolts trying to establish an Islamic country, look up Negara Islam Indonesia.
The thing is both the Dutch and the republicans did not have plans to partition Indonesia in the first place, be it by religion or race. Heck, the idea to separate New Guinea only appeared in 1947. The Colonial Minister of the Netherlands faced outrage when the politicans knew they made peace with the evuuuul Soekarno with the Linggadjati agreement. Spontaneously Colonial Minister Jan Anne Jonkman said that part of the agreement meant that New Guinea was to be separated for
Dutch settlement. Then the politicans pushed for it and made it unilaterally amended.
Come on guys, this is the early Cold War, realpolitik is abound.
To make this succeed, you need to make the Republic already in the commie camp, then there's no reason to appease our imperi- I mean nationalist revanchism.