Oh, the whole internet is using 512-bit RSA keys, like some GitHub users were? (And I did say "some" before, not "all" or "whole internet".) My point is that the 512-bit users would not have been targetable if nobody knew their keys were 512 bits long. And with bandwidth constraints, their keys would probably not have been bruteforceable either. Due to GitHub publishing their keys, they were targetable, potentially for months, plenty of time to factor.
I guess the response to that will be something about how they don't "deserve" protection because they used weak keys, and while I would resent that sentiment, I can't really argue against the idea.
To sum up, GitHub is doing something cryptographically unnecessary for this use case, that potentially harms confidentiality and anonymity for some users, and the arguments in favor seem to be: 1) A few users find it marginally useful, 2) It doesn't break the actual crypto if the users do it right, 3) Obscurity is taboo, 4) The name is "public key". I'll grant my position is weak, but so are those arguments. Their primary strength is dogma. Which, I don't know, maybe drilling crypto basics does have a net benefit even if they're not applicable to every situation.