Well, sort of - at the application level, that's true, but GHE is typically run behind a VPN. Certainly that should be the case for a company the size of Uber.
Even before GHE added 2FA, it shouldn't have been possible for a leaked set of login credentials to be used to access GHE, without some other sort of compromise (VPN cert, physical compromise of hardware, etc.).
Lateral movement by an attacker is a real thing. And while credential reuse is something most security focused web companies are trying to mitigate, a push for "sso"-like account management is seemingly undoing most of that effort inside the network if not done properly (specifically, auditing and monitoring of behavior).
This is why 2FA is important! I worked for a company that had a very similar setup: I essentially had a single "LDAP" password. But: everything web-browser went through a single sign-on site, and it required 2FA (and so, you were never entering your password into even random internal applications: there was exactly one page where you should log in). Terminal stuff had a similar flow that also required 2FA (e.g., for SSH). As a user, the experience was not painful at all.
It does seem like, however, from an operations standpoint, getting such a setup in the first place is not trivial.
> Kalanick, Uber’s co-founder and former CEO, learned of the hack in November 2016, a month after it took place, the company said.
I don't know if they were using GHE. If they were, at the time it did not come with a good way for them to enforce 2FA for users.
[0] https://enterprise.github.com/releases/2.8.0