Why is refactoring code from JavaScript to TypeScript a bad thing? Short of using a better, but non-web-compatible language, I don't really see a better option.
I think reasonable people can probably agree that there is a difference in kind between CoffeeScript and TypeScript. CoffeeScript was functionally equivalent to JavaScript, whereas TypeScript has feature-level improvements that are worth a developer's time. Sure, TypeScript is pushed by Microsoft. It's also an excellent solution for large-scale systems, its adoption is nontrivial, and Microsoft has a history of supporting its tools (Managed C++ aside, I suppose) in a way that can offer a promise of consistency on its own.
Microsoft has also been doing a good job of keeping TypeScript aligned as JavaScript++ by absorbing ES6 features into the language. I was initially worried that TypeScript would be a fork of JavaScript and eventually diverge enough that it was painful to use, but there aren't any signs of that happening yet.