I would write back to them very politely, something like this:
Hello,
Thank you for your email. I initially reacted by pulling the extension, in fear of possible legal consequences. But on reflection I would like to propose a better solution.
There are hundreds of extensions that customise websites, in many cases to help 'power users', or to assist people with accessibility problems not provided for by the websites themselves. These extensions are often made by the websites' most avid users. A great example is the Refined GitHub extension, which GitHub itself has embraced as a proving ground and source of inspiration for new official features. [1][2]
That said, it is of course vital that people understand that such extensions are unofficial, and that they are unsupported and not endorsed by the website owner.
I would like to notify you of my intent to republish my extension with the changes outlined below, which I hope will satisfy your concerns.
• New extension title: "BetterSlack: Unofficial customizations for Slack"
• Modify store description to include an explicit warning that installation and use of the extension is at your own risk, and is not endorsed in any way by Slack, and that Slack offers no support for it.
In the interests of transparency I will publish all of our correspondence on my blog, as I think this is an important issue of interest to the wider community concerning the rights of individuals to control their own computers and customise their own experiences.
Best regards,
...
[1] https://github.com/sindresorhus/refined-github/issues/1469
[2] https://blog.github.com/2018-08-28-announcing-paper-cuts/