First, I agree with the thrust of the article. However, you'll probably find they didn't set out to conceal this - the MoD beancounters were wetting themselves over the thought of huge cuts in the Defence Budget and missed a minor bit of detail.
As usual, the press miss the big story for the sake of a headline. Ask any MoD project manager what the real concern at the time was and they'll say they suddenly had to start paying for QQ (and DSTL) services but didn't receive any compensatory lift in project funding - which meant CAPABILITY had to be sliced off the other end. This was compounded by having to pay double, as DSTL demanded payment for "shadowing" their QQ counterpart.
The figures quoted are nothing compared to the nett cut in the overall budget caused by this. That is the disgrace and it is disingenuous, yet typical, of the committee raise the issue many years after the event without telling the full story.