If you uninstall the plugin and you didn’t optimize any images when it was installed, yes, your site will be exactly as it was before the installation.

If, on the contrary, you optimized some images while the plugin was installed, uninstalling the plugin will not restore your images to its original state (unless you do manually do it before uninstalling).

Regarding the message, no need to worry. That’s a message displayed by Enable Media Replace, but it doesn’t do anything other than showing a message.

Best,