Come on, with the hyperbole here... Really? The "best" thing about Nest was Works with Nest? Oy.
The best thing about Nest is how excellent the products are, how great the app is, and how consistently they all work together. I have several different Nest products and they are all fantastic. The Works with Nest program is nice, but it is about 27th on the list of things I like about Nest now.
I am not saying that it is great that this has been removed, but with security improvements there are always trade-offs that need to happen. Perhaps there is a better way to do this, perhaps not. But I really don't think this is the big deal that you are making it out to be.