I disagree. The design intention of public keys is not that they should be published along with a mapping to the user's identity, without the user's consent. It's that they may be published, or eavesdropped, without breaking the cryptography itself. See here[0] for the privacy-violating consequences of publishing public keys and identities wholesale.
That's not a failure of public key cryptography, that's a failure of the SSH protocol.
As you say, public keys were designed to solve a key distribution problem. Inherent to that problem is the idea that a public key could become, well, public. They solve that problem very well, and there is no intrinsic reason why you shouldn't just publish them because they were intended to be defensible against that very eventuality.
Practically speaking I disagree that GitHub has done anything wrong here - changing habits to diminish the publish-ability of public keys because the SSH protocol exhibits suboptimal behavior encourages further lazy security for the SSH protocol.
We shouldn't tap dance around an SSH-specific problem by claiming that public keys need to be kept secret. That's absurd, we already have private keys. Moreover, it is detrimental to other protocols that rely on publicly verifiable signatures and nonrepudiation to adopt this sort of perspective.
> That's not a failure of public key cryptography, that's a failure of the SSH protocol.
But Github is using public key cryptography as implemented in SSH - if that has a failure, Github should take some blame for not working around it, especially when they are going out of their way to expose data that has little benefit IMO.
Anyway, SSH is orthogonal to one of my points, which, phrased another way, is that publishing the link between two identities (the key itself, and the key-owner's Github profile) without consent or need is unethical because it violates the privacy of the owner. I believe there is precedent in the PGP world (e.g., "I believe it's poor etiquette to upload someone else's key to a keyserver as you deny them that choice."[0])
I sort of get the "detrimental to other protocols" and "lazy security for the SSH protocol" points, but when you talk about publishing public keys, do you acknowledge a difference between "key XYZ is in use on Github" and "key XYZ identifies user ABC on Github"? I'm saying the latter is unwise and unkind, and it would be even if the SSH protocol didn't have this particular failure.
[0] https://news.ycombinator.com/item?id=10004678