Indonesia could not terminate Obama's citizenship. Obama's mother could not renounce his citizenship, and Obama, himself, as a child could not renounce his citizenship. In other words, the US protects the child's citizenship by not allowing it to be lost, renounced, terminated, or any other word you want to use.
Indonesia does not make US law, the government of the United State does and the United States, ALONE, decides who are its citizens.
The part of Indonesian law that provides that a child under five adopted by an Indonesian father is an Indonesian citizen is automatic. Unlike other provisions, it does not require that the child take any action to renounce some other citizenship.
You are right that little Barry’s status under the Indonesian statutes did not terminate his US citizenship. It is not easy for a minor to affirmatively renounce US citizenship. And he was not required to do so under that Indonesian provision.
However, US law at the time Barack was in college provided that if an ADULT takes certain actions respect to establishing citizenship in another country (for example, obtaining a passport), then he loses US citizenship.
Did Barack, after turning 18, make an affirmative application to renew his Indonesian passport? That would appear sufficient under US law to cause him AT THAT TIME to lose his US citizenship, without the US state department necessarily even knowing about it.