Freedom of the air is all well and good until:
1. Ostensibly "random" audits always find things. We all know that an auditor can find anything if he digs deep enough, or are creative in interpretations
2. Every so often, there is a clearance that is denied to an enroute aircraft due to some magical administrative error.
As for the Americans, how many US airlines go through Malaysia / Indo as a percentage of their routes?
And same for the Europeans. Additionally, an individual airline there has the ability to say it wasn't actually us, it was the [insert other Euro country here] that drove the ban.
If QF was to be denied access to Indo airspace it would probably bankrupt them.