You're making conclusions not supported in the article.
That article doesn't support any conclusion except that the author is a douchenozzle.
Critics point out that crony capitalism can't create a true free market in the defense industry -- it's the equivalent of diet hucksters who claim you can eat yourself fitter. This is about money: pork barrel politics hiding under the noble banner of national defense.
With this assertion, the author advertises his ignorance of the GE F110/PW F100 dual engine program for the F-16 which was very successful and brought the long term costs down by orders of magnitude more than the development costs of the F110 engine. (This is not an obscure reference either. The parallels between the F-16 and the JSF are obvious to anyone who has a clue about how the JSF will be deployed.) Now every program is different and I am not saying that the JSF necessarily needs another engine, but statements like this serve to instantly position the author a couple steps outside the maximum radius of sanity and reason. Not only is it a straw man argument, when the intentionally false "free market" verbiage is toned down to "more competitive" the claim falls flat on its face - at least as a universal assertion (which is precisely how it's formulated, so it's not like I am misrepresenting it here). Developing multiple suppliers often can reduce long term costs A LOT. Not always, but often. The market needs to be large enough, service life of the product has to be long enough to allow market forces to work, and oversight needs to be in place to keep pricing transparent, but these things can be done.
The JSF engine program might be a bad fit for a competing engine. I don't know, and I definitely don't take secretary Gates' opinion lightly. However I DEFINITELY do not take at face value anyone who derides such a program based on the up front cost of the development earmarks without doing a detailed projection of the total JSF fleet costs for the next 40 years or more. That's a bit of real journalism that seems a bit above the pay grade of this particular CNN hack.
The article becomes even more bizarre by extrapolating from one earmark ridiculous abstractions about the character of politics in DC. The problem is the ENTIRE DEFENSE budget. It's too fvcking huge. It is utterly laughable to have fake lefty columnists inciting rage at one earmark which is a drop in the bucket. For anyone who claims to be against the corruption of the military industrial complex, it is columnists like this one who are the biggest impediment to any real progress. By diverting public attention from the elephant in the room they are actually helping to support it, despite claiming with all their fake fervor to be battling against it.