If you have to change the root of the active page for some reason: The Document Root entry would have to be changed (not directly accessible through Virtualmin for existing servers - you need to use Services / Configure Website / Document Options), and possibly a redirect for “/” to “/version2” is required so that the correct version is loaded when a user fetches your URL with just the hostname.
Even better, but also more complicated, than a redirect would be using Apache’s mod_rewrite; then the user would not see the “/version2/” in the URL path.
All in all, moving directories indeed would be easier.