For those that aren't familiar, we have both passive and active sonobuoys/systems. Of course this article is addressing the use of active sonar systems, but I am surprised that it didn't mention any specifics (or maybe not surprised). I would imagine that this is specifically against Medium Frequency Active (MFA) sonar systems, primarily used on surface warships. As a former exercise officer, I can definitely validate Gatordev's comments, the amount of sonar energy put into the water is ALWAYS taken into account while setting up for training and exercises, especially with multiple warships, submarines and P3s going active. Computer assessment software is used to that compares location, migratory patterns, energy and frequencies used, and you can assess impact and if it is necessary to set up ping schedules for participants.
As the OCE (Officer Conducting Exercise), you are responsible for running an analysis of time and energy put into the water column by various systems (LFA, MFA, HFA, EER, etc). The current rules that are in place are followed, and the appropriate control measures, and marine mammal mitigation are used, but you still have civic organizations that continue to seek to abolish all use of active systems that the warfighter needs. Targets continue to have lower source levels (quieter), and ASW as a whole is working towards improved systems to search, localize and track, sometimes in very difficult environments (littoral, sea states, shipping, etc).
In the end, there are different approvals out there that govern our actions, and are built into our CONOPs and are in place at the unit level (marine mammal lookout anyone?). We definitely honor host nation/international EEZs, fishing rights are a huge deal both with our country and others (Japan and Australia). Other systems, such as LFA, have their seperate approvals in place.
As mentioned, during real world operations all bets are off, and use of these systems are not constrained. All in all, a moot point, we have been dealing this for quite awhile, and as long as these systems aren't banned outright, the Navy will continue to work within the guidelines, and get training done.