As far as I can tell, the key hope for the plaintiffs was the National Environmental Policy Act. According to Slate Magazine:
Over nearly 40 years, the court has heard some 16 cases related to the National Environmental Policy Act and ruled against environmental interests in every one.Basically, the plaintiffs needed to show that the sonar activity was more detrimental to the environment than beneficial to the public interest, whereas the Navy had to show that 'national security' was more important than the affected marine life. Unsurprisingly, Chief Justice Roberts argued that the military needed 'effective' military training, and that the environmental claims were unsubstantiated and silly. This decision (Supreme Court Opinion) has been nicknamed the 'kill the whales' ruling.
So why the 'unexpected' undertones in major news pieces? My guess is that the case foreshadows a not-so-friendly attitude towards environmental issues that trouble green activists and journalists. The current makeup of the Court attributes a certain frivolity to cases like this one, which doesn't bode well. Such frivolity is unwarranted when considering the empirical studies that show sonar is bad for whales. And the decision backs up claims that the Court is unlikely to question matters of 'national security.' That being said, this case didn't exactly give the Navy free rein over its projects, and they will have to write Environmental Impact Statements for sonar training in Hawaii, the Southeast (with proposed sonar training grounds off the NC coast), and even California.