SUGGESTED FIX

Update CustomAction.idt table to mark the CustomAction with the appropriate elevation privilege.
                                     

EVALUATION

I found that the "JavaControlPanel icon disappeared" issue was caused by the missing jpicpl32.cpl in the system32. The java.exe, javaws.exe and javaw.exe also disappeared in the system32 after uninstalling 5.0u7. The problem was that the Java(5.0.u6) system files did not get copied into system folder. 
It was the bug in the installer that the uninstall CustomAction was not marked with the appropriate elevation privilege. For windows Vista, when you are logged in as user in the Administrator group you do not have all privileges of the built-in Administrator user. The  Windows installer will elevate portions of the install to system privileges necessary to install the package. If the CustomAction requires elevation but is not marked appropriately then the CustomAction will fail.

I did noticed that if IE was open before uninstallation, Sun Java Console did not load after uninstallation. But, if you reload IE, Sun Java Console will load correctly. 
If the Sun Java Console does not load,  restart the IE will solve the problem. It is the issue of the IE refresh.

I could not connect to your system with remote desktop
The system I tested in our lab:
Vista: Evaluation Copy 5308
                                     

EVALUATION

I have followed the steps to try to reproduce the problems. The evaluation results were as the followings


1. Open IE and click "Tools - Sun Java Console", the Java Console will not be loaded.
I could not reproduce this problem. I tried install and uninstall a few times. Java Console loaded all the time after uninstallation of JDK5.0u7

2. Goto control panel and open Java Control Panel click "Java -Java Applet RunTime Config -View",JDK5.0u7 is still there.
This issue was not particular problem for vista. It happened on all of the systems. It was the issue of the refresh for "Java Applet Runtime Settings" on opening the first time after uninstalltion. It is the same issue as the bug of 6343129. 

Current work around:
The view will be set correctly if the user click OK on the view and click Apply on Java control panel.

Please retest the first issue(load Java Console) and let me know if you still have problem. If you can't reproduce the issue, I would like to close the bug as the duplicate of 6343129.