No, I actually use the same vbscript that I embed in the MST - along with its main purpose to remove the JAVA start menu folder, I did add few lines that call a batch file from a network share (on our deployment server), using the xcopy command to dump the whole Directory Sun (with subdirs Java, Deployment, and the files there) in Windows Folder. The batch file has a IF statement, so if the Sun directory already exists, it will just exit without any actions; otherwise it will deliver that content.
I figured the MST can be handy for pushing future JAVA updates, as BOTH actions in the embedded vbscript (Remove Start Menu Dir and Deploy system-wide config) are conditional, and if there is no need to apply them, they will be skipped...