Even if this is so (and I am not conceding the point), applying for, receiving, and using an Indonesian psssport were actions taken by Obama himself.
If he, in fact, did so. The whole passport story stems from the claim that U.S. citizens were forbidden from traveling to Pakistan in 1981 and so Obama must have travelled on an Indonesian passport. In the first place that wasn't so, citizens may have been warned not to travel there but there is no evidence supporting the claim that they were forbidden to travel there. In fact during the first half of 1981 the U.S. was announcing multi-billion dollar aid packages for Pakistan and talking about resuming delivery of F-16's. Secondly, Obama left Indonesia when he was 10 and never lived there again. How and where did he get an Indonesian passport? Finally, dual citizenship is not against the law, so even if Obama had a foreign passport it would not count as an expatriating act. He would have had to formally swear allegiance to Indonesia and disavow any further loyalty to the U.S. Since he was in school at the time that's highly unlikely.
Holding more than one passport is perfectly legal and does not threaten one's status as an American citizen. I hold three.