The java debugger will allow you to kill a thread by injecting an exception into it.
Start your Java process and have it listen on some port:
java -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=4444 <Your Program>
and connect the debugger with something like:
jdb -attach 127.0.0.1:4444
and issue the following command:
threads
to get a list of the running threads, and use the kill command to kill a running thread.
kill 0xe2e new java.lang.IllegalArgumentException("er");
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