One thing I am not sure is why such a radical action was taken so quickly without thinking carefully first? It's not like a lawsuit was threatened or something. The original request in
https://github.com/minad/mimemagic/issues/97 that you linked to was very polite and professional.
1) A time extension to remove the GPLed code could be politely requested. I know that the copyright belongs to all contributors but getting on good terms with the maintainer could be a solid first step. I think just opening a PR with that file deleted (and tests failing) could have been interpreted as a willingness to comply with the request in good faith.
2) A request to relicense the XML file in question under LGPL could have been sent to the original project (could be problem without CLAs, but still worth a try). Then the library could have been relicensed under LGPL.
3) Gem users could have been notified. Some prominent people from those projects could have helped with (1) and joined a kind request (2) to the original project.
At least that's how we'd (try to) handle it on our project under Eclipse Foundation (though we used to have a GPL code scanning for releases in the first place until very recently) if such situation arose. Anyway, talking to people first before doing something quickly is often a good idea.