Instead of using SoapServer::setClass()
you could use SoapServer::setObject()
and pass your service in:
$oSOAPServer = new \SoapServer('/path/to/wsdl');
$oSOAPServer->setObject($container->get('my_service'));
$oSOAPServer->handle();
Implementing a soap server is documented in the Symfony documentation: How to Create a SOAP Web Service in a Symfony2 Controller
Also, if you only need a repository, don't inject the whole entity manager. Register your repository as a service and inject it to your service.