What's most interesting about that article is that IDW apparently had a planned Doctor Who book with Mark Waid writing.
That's not surprising. We knew that IDW had plans for 2014, including another Star Trek
crossover. (They announced it at NYCC last year.)
IDW undoubtedly knew their license was coming to a close at the end of this year, but they probably expected a renewal. Either the BBC wasn't happy with working with IDW, or the BBC realized they could get more money out of the license and then priced it out of IDW's range. I think the latter is more likely than the former.