Sure, they are working towards the benefit society. Anyone who has a job can justifiably claim so, unless they are doing something really evil/wrong. How? That is already covered by Friedman and Rodgers. When you work, you contribute to society in a particular way, and you can/should be proud of it.
Let's get back to Whole Foods. What is really the motive behind a business such as Whole Foods when they do something such as donate their 5% profit? Mackey gives 1 reason himself: "There can be little doubt that a certain amount of corporate philanthropy is simply good business and works for the long-term benefit of the investors." There, so 1 reason is precisely because it benefits the business, thus it benefits the shareholders. The business gains goodwill, an intangible, not taxable asset capable of generating future profit. Nobody is advocating that you should not love your society and donate a little. What's essentially being argued is your core interest. And to pretend that the investors don't have anything to do with it, well that's really just a cloak to disguise business motives.
If the core interest does not involve the shareholders, what happen if the business falls on hard time? Whole Foods may be doing well, but like I said before, what if it donated more and not getting the publicity/customers it wanted, while the business itself is failing? As a business goes through hard time, it will realize the importance of the shareholders interest, to avoid being out of business, which would serve society no good. Which is pretty much why Rodgers called Mackey's article: "How Business and Profit Making Fit Into My Overarching Philosophy of Altruism." To Mackey, what he thinks he's doing leads to profit. To Rodgers, it is profit that leads to what he did, and I agree.
Mackey also claims that it'd be justifiable even if his donation program did not generate PR/profit. To which I don't agree, on what grounds would it be justifiable when you are using someone else's money for your own interest? And also the part where he claims he "hired" his investors. I think Rodgers already talk about that. He can afford to say this only because Whole Foods is doing well. The donation program happened to serve the business needs but that doesn't mean the opposite.
Perhaps I'm not doing a very good job of explaining myself, but Friedman and Rodgers do have very good points in that article that pretty much sums up everything.