They should have assumed it. While I agree they can't be expected to have enough technical savvy to remove watermarks, they should have re-typed it and hid or (better) destroyed the original.
What she did was illegal and the government is going to nail her to the wall for it, if for no other reason than as an example to others contemplating the same thing. I'm astounded how little effort they (both the leaker and the Intercept) put into avoiding discovery.
If it were me the watermarks would have been gone before the document left my possession. If you depend on other people to keep your secrets you're doomed.
My first thought is that even blogs like AndroidPolice protect their sources better than The Intercept does here - they go as far as re-creating screenshots or renders of phone leaks.
The Intercept's lack of care is astounding. There wasn't any reason they needed to publish the fact that they received printed copies, let alone the actual scans.
I don't think we should expect news outlets to scour every printed document for these watermarks and remove them. Most aren't that technically savvy and this solidly seems like the responsibility of the person doing the leaking.
Leaking is dangerous and risky. I don't know the leaker personally but I could understand someone feeling that documents need to be released to the public and, at the same time, feeling like they can't evade the NSA's investigation. At that point any counter-measures probably seem pointless, especially for those who are not technical and can't imagine any bounds to the NSA investigative powers.