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From your error message, I think you forgot to update the agil_moveit_config/launch/kuka_kr6r900sixx_moveit_controller_manager.launch file. That is the file that actually uploads the contents of the config/controller.yaml file, and sets the moveit_controller_manager to the correct value.
Without that, MoveIt won't know how to interface with your controllers.
I've also just created an example MoveIt configuration package for the KR 6 R900 sixx, see the kr6r900sixx_moveit_rsi_convenience in my fork of ros-industrial/kuka_experimental. I've added a bit more than just a working configuration, so please test it out and let me know if it works for you.
The main issue is that the kuka_rsi_hw_interface doesn't (by default) setup all the topics and services that the tutorial you followed to create your MoveIt configuration expects. Especially the namespacing of the action server and naming of the joint state and feedback topics is different. The structure I set up in kr6r900sixx_moveit_rsi_convenience takes care of that, so everything 'above' kuka_kr6_support should now be able to interact with the RSI hardware_interface as it would with a regular ROS-Industrial driver (but see also the comments in the launch files).
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