When deploying a large Java webapp (>100 MB .war) I\'m currently use the following deployment process:
We upload the new version of the webapp to a separate directory, then either move to swap it out with the running one, or use symlinks. For example, we have a symlink in the tomcat webapps directory named "myapp", which points to the current webapp named "myapp-1.23". We upload the new webapp to "myapp-1.24". When all is ready, stop the server, remove the symlink and make a new one pointing to the new version, then start the server again.
We disable auto-reload on production servers for performance, but even so, having files within the webapp changing in a non-atomic manner can cause issues, as static files or even JSP pages could change in ways that cause broken links or worse.
In practice, the webapps are actually located on a shared storage device, so clustered, load-balanced, and failover servers all have the same code available.
The main drawback for your situation is that the upload will take longer, since your method allows rsync to only transfer modified or added files. You could copy the old webapp folder to the new one first, and rsync to that, if it makes a significant difference, and if it's really an issue.