Hi Jay,
I've fought and fought with trying to use agent connection status for JVM availability, but there are a bunch of caveats.
As mentioned above, cross domain groupings and you have to use agent clusters, that leads to even more issues. Agent load-balancing and now your collectors are having to run java script calculators to try to determine if the agent was there in the previous time slice. In my experience, not a good use of the APM.
After beating my head against the APM versus Infrastructure rock enough, we started to move all of the availability type questions to SiteScope. Basically saying that if the answer is on/off, up/down, present/not present then that is an infrastructure monitor. If it is how well, how much, how long, trending, performance style questions, that is the APM.
There is no sense in pounding a square peg into the round hole.