While you technically can do anything with Java that you can do with any other language, I think this is a serious mistake. If you are the sysadmin, and will always be the sysadmin, then by all means, do what you like. But if there is any chance, however small, that the system will grow and be put in production, and managed by professional sysadims, then
you should do it using the "when in Rome, do it the Roman way" approach.
For Linux, the Linux way is perl or bash scripts.
Plus, perl is a useful language to know. You can do many sysadmin things in five lines of perl that would take many times as much in Java.
p.s. you are showing your Windoze biases talking about "registry" as there is no such think in Linux, BSD, etc. All that stuff is kept in ascii text files.