I only skimmed the article, but I'm not particularly scandalized by it.
I spent 10 years as a contractor for DoTreas (GTE, then Verizon after BellAtl merger). IRS was one of my customers and I spent a lot of time working with that bureau.
Since then (7.5 years), I've worked for a large multi-national IT services firm with large customers worldwide.
NOTHING in that article is unique to IRS or FedGov. Large corporations (and many smaller ones) are just as guilty of it. If you think a profit-driven company is necessarily better with money or resources than FedGov, you're deluding yourself. You don't hear about it, because you don't have visibility into the inner workings like you do with the Govt.
FWIW, many of the IT folks I dealt with at Treasury were more competent than their peers in private industry. I know that goes against the common perception, but it was my observation. There was a real sense of mission and fiscal responsibility at the various management/director levels rather than profit-driven motives. While my experience in private industry was "how can we do it cheaper", the govt was more about "doing it better" or at least "doing it better within these budget constraints" (the latter seems identical to the "do it cheaper" idea, but it's more about staying in budget rather than cost cutting for profit's sake).
Oh, to Ben's point about people, FTE are the largest cost center in my world as well. We're moving a LOT out to India because you can get roughly 5 "Specialists" there for the price of 1 in the US ($15k vs $95k).
Chris