Perhaps I missed this in the article, but in what "cases" are the people deciding whether to continue funding complex systems research not scientists?
My guess is that a majority of the research into complex systems is funded by the NIH and the NSF. Both of which make funding decisions largely based on the opinions of other scientists.
The saddest thing about it is that I'm positive there's something to the theories involved, but they're being squandered by people more interested in the popular appearance of success than they are in true efficacy -- possibly because they ego-identify with the successes of their pet projects, and ensure that they don't pay enough attention to the right factors to recognize the difference between appearance of efficacy and true efficacy.