I doubt the support costs were very much. As with all things Google other than being an adsense buyer, support was basically "send us an email and we'll respond with a robo-faq that may or may not have anything to do with your question".
And Google Apps was actually quite easy to setup, partly because Google documented it pretty well but mostly because many DNS providers would basically do a one-click Google Apps setup automatically for you.
Given that there were people who would try to use the free version for their business, and then kvetch (on HN and/or other major technology blogs) when their account was hijacked and they lost business critical access and couldn't recover quickly because they didn't have the 24/7 phone support, it might actually be better that the free version is getting sunset....
Frankly, I read the blog post and I have Google Apps for Business at work (and use the free version for my domain), and I missed this. It's kind of buried in the middle paragraph, and I don't remember it being trumpeted on the upsell page when I signed up.
If it's anything like the Play Store phone support, it's basically a placebo so you feel instantly gratified, while the CSR sends an email to the real support team ( with ~48 hour turn-around).
This is likely primarily an opportunity to upsell other services - great opportunity to chat with people, make a connection, build a relationship, etc..
And Google Apps was actually quite easy to setup, partly because Google documented it pretty well but mostly because many DNS providers would basically do a one-click Google Apps setup automatically for you.