When deleting an original image, all of its derived images (transformed versions) are deleted as well.
However, Cloudinary supports incoming transformations, this will transform your image before storing it in your account. So you can upload the original image, while transforming it, here's a PHP code example:
\Cloudinary\Uploader::upload('/home/my_image.jpg', array("width" => 1000, "height" => 1000, "crop" => "limit"));
Then you can either deliver this transformed image as is, or create any further transformations that you require (e.g., thumbnail).
The original image will never be stored in the first place.