Mixing up two very different incidents there PA.
I am referring to the forced Indonezianization of the Chinese community under Sukarno and Soeharto, where Chinese-Indonesians were expected to adopt "Indonesian" names and overt displays of Chinese culture were banned. This was an ongoing process over the 1960s and 1970s and didn't involve any wide-scale violence as far as I am aware.
Your link refers to the anti-Communist purge of 1965-66. I will question your figure of 500,000 to 1 million victims, I know that is the accepted figure but in fact nobody has the slightest idea of how many people were killed and for a variety of reasons I think the actual number is closer to 100,000.
However, despite the wiki claim, this was not especially targeted against the Chinese, not even nearly. The vast and overwhelming number of victims were kampong-dwelling Javanese, Balinese and to a lesser extent Bataknese villagers, mostly killed by their Red-hating (or whipped up to hate the Reds) neighbours using pangas and any other agricultural implements that they had to hand.
The Chinese did not suffer especially heavily in those purges, despite the Indonesian Communist Party being heavily influenced by Beijing at that time.