That's underhanded for any media publication that aspires to the idea of "journalism".
In addition they could have at least mentioned the idea that other theories emerged as to what the slides they presented might actually mean that way people would be aware that there were other valid conclusions that could possibly be drawn, especially by those with tech and government experience.
Seems to me that the claim from the article re scare quotes is nonsense.
There are no scare quotes in the guardian piece. There are, however, lots of quotes.
The things that the article claims are scare quotes (the relevant passage "...That has allowed the companies to deny that there is “direct or indirect” NSA access, to deny that there is a “back door” to their systems, and that they only comply with “legal” requests...") are, if you actually read the guardian's article and see the context, clearly terms quoted from the companies' denials (given more fully earlier in the article), the point of the passage being to explain why the companies denials were true given the specific terms used.
It's hard to lie effectively when you don't know how much of the truth is known.
That's just guesswork, of course. I think it's easy for us (and the Guardian) to imply a lot of detail where none exists. I don't think the Guardian has anything to apologize for. It'd be great if we all got a better technical view of these systems. But asking to receive it third-hand through a leaker and a non-technical reporter is probably a bit much.