Fair point. I've always used the approach of dedicating a machine to one particular application (using virtual machines once those became available), so the impact of upgrading the a global JRE is limited.

I did once work on a system where we installed two JREs in parallel, and selected which one to use for the app based on an entry in the manifest file. That let us upgrade Java versions under application control, without requiring sysadmin intervention. Took a couple of lines of shell script.