Without really being qualified to answer, I somewhat disagree with the articles. Kind of a chicken or egg argument here. Deliberately drawing in does make it harder to do things with your lower back and that is what Pilates does; it makes you develop, for instance, upper back muscles so that you carry more on your upper back as opposed to your lower back. When I draw in I instantaneously engage my upper back. Sitting in a office chair all day also weakens your lower back, so NOT doing Pilates is just as evil. On the other hand, the article points out something that I think Pilates practitioners should take into consideration.
I had a really good instructor in Chicago. From what he taught me, Pilates was done on even amputees so, if there is a back problem (or limb problem), you work around it and if you tell your instructor what issues you have, they will act appropriately. I had sciatica and worked my way through it with a chiropractor first and conservative medical treatment (NSAIDS). Eventually, it went away on it's own with daily treadmill and stretching.
Having a vested interest in conditioning my body to never have a problem like that again, I asked around and a friend recommended a Pilates instructor. In the initial meeting I told him exactly what I had been through. "Sciatica," he said "that means to me that we are going to have to limit unsupported forward movements for a while." "We can work around anything by doing another exercise" The beauty of Pilates, he said, is that if one thing cannot be accomplished there are many other ways to engage the same muscles. So the goal is to make movements efficient by training until you get what you need and this is why it is so important to work with a professional.
I will say this though, my instructor always said that I had a superior sense of my body movement and was very responsive to his commands. He once told me, "Damn, you are good, I had to work with a client for ten minutes to do what you just did" Why do I say this? Those who are aware of the movement of their muscles are, I think, much more sucessful at and have more to benefit from Pilates. Self proclaimed "palsies," be careful. Unaware, haphazard, unfocused, and lax moves can in fact hurt you.
So, I think the article could serve as a warning if you read it right, but as with many journalists, they get your attention with "The Sky is Falling"