I have interpreted this request to be something like this:
When enterting an item that would produce a duplicate URL, we would receive a warning message, error alert, pop up notification (something) to alert us to the conflict, RATHER than creating a -1 version of the URL.
Instead of a using popup that gets in the way how about just putting a warning message on the URL field. In the same manner as when a required field is not filled in. Here is my idea pictured below. The top shows the current error warning behavior. Then my suggestion. I used warning instead of error and the url fills in with the -1 but the warning message gives the duplicate url. The user can then change the name or url or they can submit and the -1 will be applied.
I also want to make sure that the current behavior of adding a -1 at the end of the URL stays. I have a custom module for a client where the title field is set with a hidden field on the front end. This is because all the fields needed for this module are dropdowns or dates.
I like the error message at the field too. I guess it depends when the validation occurs though - upon save or after entering the URL.
If it needs to validate on save, I’d prefer the notice be more prominent, like a pop-up.