How to make View setting changes happen simultaneously with deployment of a template
You can export a view, via the views interface or the Features module. Both will version control the view, updating the view but chaining/updating the code (if no alterations have been made in the UI).

What I usually do, is to use a script that


Updates the code on the
Reverts features
Clears cache
Runs cron


This is done calling drush commands and works very well for updating sites that doesn't rely heavily on cached data.