I don't like SAFe for many reasons but I have seen it used successfully as an agile steppingstone. Some of the more original ideas with in SAFe (there aren't many) can even be useful. Anyway I don't think the idea of an ATO is a bad idea or anti agile. Even within an agile environment projects can exists and can be done in an agile way.

Due to badly run prince2/PMI projects people are allergic to anything remotely sounding like a project. So I get the autor when he thinks of ATO == PMO == PMI == waterfall == nightmare. But for larger organisation you will properly need something like a ATO to be successful. Like anything else a badly run, top down driven ATO will fail and make life difficult for anyone involved (this is also made clear in the original McKinsey article).