The article is about extending the PHP to the backend enterprise Java world, a native JMS for PHP will not serve this purpose and will not give the PHP the abilities that are needed for this task.
I agree that the PHP/JAVA extension is costly (not to the extend you describe it but still costly). In the next release of PHPMQ I intend to implement the messaging interface over HTTP. This will eliminate the need for the PHP/JAVA extension.
Speaking of cost ... MantaRay is unique in that it uses a server-less, purely distributed architecture. You do not need a costly centralized broker (with load balancer and backups). Remove the centralized broker and you remove this single point of congestion and failure, you get better performance and a more durable system.
Having said that, PHPMQ is an opensource project and the PHPMQ messaging interface is well defined and decoupled from the implementation, you are more then welcome to contribute code connecting PHPMQ to any other JMS provider.