At GitHub, we faced the same issue when ZenHub [1] came out with their chrome extension. While, Slack is well within their rights to _ask_ you not to modify their user experience, it's short sighted of them to do so.
With ZenHub, we worked with them even closer because we saw that our users were happier using GitHub + ZenHub. We made it super clear that UI changes would likely break their app but that would be a risk for them to evaluate. In the end, it worked out well since ZenHub invested alot in their UI and became a long term partner of GitHub's.
From a technical level, I'd also take issue with this. You're customizing the output of their services once it's in the browser at the request of the user. If you're still interacting with Slack through the API and being a good platform partner (i.e. respecting rate limits), then I think you should be allowed to keep on. Disclaimer: I'm running a company on the Slack platform [2]