Shutdown behaviour is quite different between stopping ESB with CTRL-D or doing a kill on the process (not kill -9)

We have the problem that we launch Fuse ESB inside Fuse IDE by directly invoking the Java class instead of calling the batch script. So for stopping we don't use the delivered batch script but we end the process via

process.terminate();

The behaviour seems to be quite different on shutdown as it seems only parts of the shutdown process are covered inside the shutdown hook. Please see the linked issue for more information.
Can we improve the shutdown hook so it makes no longer a difference if we kill the process or use the shutdown script?

Guess that needs to be fixed in Karaf.