True - Indonesia while being an Islamic country was notorious for corruption at one point to the extent even cheques were accepted for payoffs.
However, key to the failure of Pakistan is the lack of impact by corruption/nepotism and otherwise due to a constant in flow of loans and aid which shielded the population from total collapse otherwise along with normalization of corruption as a way of life. In every aspect, Pakistanis embrace corruption not just in monetary form, but in their religious and cultural values as well.
Talking about Soeharto period, their successful economy growth compared to Pakistan is because Soeharto period has focus on economic growth. When he raise to power, what he did also make the region peaceful and this is why ASEAN is created with the first ASEAN meeting held in Jakarta and Jakarta is ASEAN Headquarter.
He is not like Soekarno who spend much money on military and made war with British/Australia/Malaysia/Singapore/New Zealan during Ganyang Malaysia campaign.
Despite Soeharto did invade East Timor in 1977, he never did that again into other neighbor. During that time he did that as Indonesia is part of Western coalition against Communism and East Timor during 1977 is regarded as almost captured by their left wing power. So saying only Pakistan that become the ally of Western power during Cold War is not true, Indonesia even invaded a country because of its anti communist agenda. Indonesia cut diplomatic relation with all communist power during Soeharto period, only in 1990 (the fall of Berlin wall) we have diplomatic relation with China again, and then Vietnam.
This corrupt regime makes the economic growth is not sustainable, SOE is also corrupt during that time, then we see Indonesia collapse due to not able to withstand from Asian Financial Crisis. After this period we made several reform that include its anti corruption agenda. The fight against corruption is not getting instant result, but it is a gradual process, and I believe the fight against corruption is also helped by the raise of our society increase religiosity as Islam is against any injustice, bribing, corruption, etc
COLD WAR: Operation Lotus | Indonesian Invasion Of Timor-Leste 1975-1999 | Historical Map
The Next level animated historical map | On 1974 Western fears that victory for the left-wing Fretilin in Portuguese Timor would lead to the creation of a communist state on Indonesia's border that could be used as a base for incursions by unfriendly powers into Indonesia, and a potential threat to Western submarines, One years later Indonesia's President Soeharto declared invasion to East Timor under support of US and Australia.