I'm not a big fan of Java. The promise has always been great, but it always seems like the reality falls a bit short. Of course, I've only used Java as an applications platform, not as a development platform or as an embedded OS.
But ignoring my opinions, I wouldn't think that running this on a Zynq would be out of the question. I would think that a FPGA based ARM (hard or soft) would be an ideal use for a JVM like this.
This is certainly not the industry's first small JVM.
Lejos has been doing this for ages: http://lejos.sourceforge.net/
Lejos is about the same size on ARM. Lejos has been running on ARM micros for almost 6 years and on H8 for much longer than that.