And the media never gets anything wrong, right? :)
(I have no idea what they got access to or didn't)

Remember, this order is the result of a court proceeding - not just media coverage (and I agree they often get legal issues wrong). So if the only information anywhere in the Treasury payments systems is all completely hashed and contains no personally identifiable information, they'd have the chance to show that. Because the judge ordered that they couldn't access personally identifiable information, though, it's pretty likely that Treasury wasn't able to demonstrate that to him.

But you do have an expectation that your data won't be shared outside the agency.

Not necessarily. Why should it be a secret that USAID is paying for this or that? Why isn't it in the public interest that the US government is funding X or Y?

Because there's a statute that says that the agencies have to protect your personally identifiable information. This issue arose in regards to the Treasury payments system, which is going to contain things like bank information and account numbers and things that go well beyond "Agency X is funding program Y." There's a law that says they're not allowed to share that kind of information, so you have an expectation that they won't. The IRS doesn't share your tax returns, the VA doesn't share your medical records, and Treasury doesn't (or shouldn't) let people from other agencies access a database that has your personally identifiable financial information.