Nope, because the tech was developed by a military contractor doesn't mean that the US government can get to the scan data on your phone. The article appears to be clutching at straws and whilst im not saying the facts given are wrong, there isn't any technical evidence that it's actually happening.
Firstly, how would they get the scans off the phone and back to the US government? When IOS versions are released devs spend a lot of time taking it apart, looking for hidden features or hints to upcoming products, but so far no one has found any part of the OS which would enable the transmission of fingerprint data, neither has anyone mentioned any trace of IOS sending any data to either government or unknown sources. Both of these implications would be a massive deal and most likely front page news, but so far there is no sign of it. Implying this may be true could also imply Siri (originally developed by DARPA) could also be stealing privacy data and two years on we have no reason to assume it's happening, heck if you look in IOS code you can find Siris web server address.
As far as i can see it, the only real risk of a security breach would be from Apples Server Farm and not from your device and even then, if that's true (and we have no technical evidence for it either) it discounts the relevance of the linked article anyway.
I wouldn't lose any sleep over the possibility