I have done a lot of testing with updating Java and I have never had an issue updating it.
One thing you can try with it is updating it using the MSI as opposed to the work around thing that Desktop Central does. This might yield better results for you.
In my experience, most exe's are smart enough to get around the issue you are describing.
Another thing you can try is killing the process prior to attempting to run the update. I had to do something like this for updating Greenshot. It starts on start up so in Package I put a script to "run before installation" that looked for the greenshot exe and killed it, then the run the update.
