Earlier quoted context omitted.
I'm not sure what you want to do. Is your problem that you do want to see the native Java classes, or you want to hide them and focus on the Ruby code? Or is the key thing you want a Java flame graph?
Java classes and a flame graph would be nice sometimes. I really only know how to use pry and Virtual VM with JRuby.
http://techblog.netflix.com/2015/07/java-in-flames.html
I'm still puzzled that there seems to be no simple gprof-style graph profiler included with the JVM.