Hmm, good point.
In early unreleased versions I did indeed provide a way of stopping the restart operation from happening. I removed it for simplicity, but now I can see it's useful.
I have just committed in SVN revision 472 this change and created Jira issue https://jira.springsource.org/browse/ROO-428 for it. The following now works against SVN trunk, and will in Roo 1.0.0.RC4 and above:
Thanks for the suggestion.
addon uninstall old.zip --automaticRestart false
addon install file:target/new.zip