The new version of Chrome will auto disable extensions that are not from Chrome Web Store, and cannot enable it manually in the chrome://extensions
page.
How to enable the extensions and disable the "auto-disable" mechanism?
You can't disable the warning behavior.
You can, however upload extensions as private to the web store and install them from there, without suffering from any warnings/popups.
You can also enable developer mode and load unpacked extensions, but then it'll pop a warning every single time you start Chrome.