Steps to reproduce:

• I installed and activated the plugin, then followed the activation procedure in the admin panel of my website. The site was successfully activated, and a .git repo with an initial commit was created in the project's root.
• Then I took a look at the CLI, and the first command was "wp vp activate". I decided to run it, for no particular reason.
• I was surprised to see that the command attempted to "activate" the site a second time.

Suggestion:

Add a check for "VersionPress::isActive()" at the start of the activate() function, and if VP is already active - print a log message and quit.