What do you want to do?

A. Remove the file and never use it again

If so, remove it from the template including it, ie https://en.wikipedia.org/wiki/Template:Copy_to_Wikimedia_Commons. Wait a few days, try again to delete.

B. Continue to use a file with the same title, but without unfree content

Here the method used on Wikimedia Commons:

1. Upload a new version of the file to overwrite it, without unfree content at the same.
2. Purge the history using change visibility links to delete former potentially non free versions.

C. Use the Wikimedia Commons version instead

I'd recommend to do B right now, using the last Commons version.

Then, copy it under a new name, on en. or Commons, then back to A: edit the template and wait some time. You'll then be able to delete it. Revert the template to the original filename.

Okay, I've read the discussion about the evolution of en.wikipedia position about local copies for protection purpose.

You're trying to solve two issues:

1. a copyvio one, for which solution B is appropriate
2. a policy one, for which solution A is a kludge, but will work to fix the consequences of a technically problematic policy choice made in the past

Technically, if we act server side, the maintenance script would, to quote the documentation, "erase the page record from the database irreversibly (you cannot use standard undelete functions to restore it)". So that would be a bad idea to request this deletion. Oh, and "[that wouldn't] update link tables, which means that links to and from that page will still be present in Special:WhatLinksHere queries, for example". The link table on en.wikipedia is too huge to reasonably update it as a whole afterwards, we would need a custom maintenance script designed for this situation.

That leads me to confirm to use regular MediaWiki capabilities is better.

So I'd strongly suggest you try A, then B. I can guide you in the whole process if you need assistance, let's get in touch on IRC.

What I want to do is C, so I've created a temporary copy of the Commons image and pointed the template to that. The deletion itself is not particularly urgent.

We'll see how that goes. Thanks for your assistance.

@MER-C Looks good to me according https://en.wikipedia.org/w/index.php?title=Special%3AWhatLinksHere&limit=500&target=File%3ATo+Commons.svg&namespace=6

Let's retry if you can delete it now.

File deleted. I'll leave this open for you to decide whether there are any wider performance implications exposed here. Thank you again.