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I wouldn't be so eager to jump in and try to force VM (java...) to be regular applications though. To a certain extent, we 'trust' our OS, our hardware to be perfect while programming. In a similar sense, you should eventually be able to 'trust' your JVM. Things like memory protection...aren't really relevent in a VM like java.
Oh, but if there is one thing that history (and security researches) tells us, it's that programs have bugs. They always do, and they always will, and nothing you do can change that.
Putting the VM into its own context is an additional security measure, that will greatly reduce the significance of any kind of exploit (or instability) that can be achieved via bugs in the VM.