Does it actually wait for a ctrl-C, or would it also exit via ctrl-D?

If so, that means it exits on the end of stdin, and your fix would be to simply run it as

system "/usr/java/jdk-1.7.0_4-x86_64/bin/java -jar 'ProgramName' < /de
+v/null"
[download]

You might have to do something more complicated, as you suggested, but it's probably better to try this easy option first.