The article is from 2009 and much work has been done in the past 2 years to study and eventually mitigate this problem. The process began years ago and one landmark year was 2008 where we find:

USA ratifies international rules on air pollution from ships

The United States of America has become the 53rd state to ratify Annex VI of the International Convention for the Prevention of Pollution from Ships (MARPOL), with the deposition today of an instrument of ratification with the International Maritime Organization (IMO).

Annex VI, which was adopted in 1997 and entered into force in May 2005, regulates the discharge of atmospheric pollutants from ships. Among other things, it set, for the first time, limits on sulphur oxide (SOx) and nitrogen oxide (NOx) emissions from ships’ exhausts; prohibited deliberate emissions of ozone-depleting substances and put a global cap on the sulphur content of fuel oil.

This latest ratification, which brings to 81.88 the percentage of gross world merchant shipping tonnage covered by the aforementioned regulations, comes as a detailed review of the provisions of Annex VI is reaching a conclusion.

Continues.

More recently we find:

NOAA-led study: Air pollution caused by ships plummets when vessels shift to cleaner, low-sulfur fuels
September 12, 2011

New clean fuel regulations in California and voluntary slowdowns by shipping companies substantially reduce air pollution caused by near-shore ships, according to a new NOAA-led study published online today in Environmental Science & Technology.

The study examined a container ship operating under a 2009 California regulation requiring that ships switch to low-sulfur fuels as they approach the California coast, and also adhering to a voluntary state slowdown policy, intended to reduce pollution. The research team found that emissions of several health-damaging pollutants, including sulfur dioxide and particulate matter, dropped by as much as 90 percent.

[…]

The project was funded by NOAA and the California Air Resources Board and conducted in close collaboration with the Maersk Line.

“These scientific findings clearly demonstrate that ships off our coast now emit significantly less sulfur pollution than in the past,” said California Air Resources Board Chairman Mary D. Nichols. “This is good news for California and for the nation. When the federal regulations kick in for ships to use low-sulfur fuel, communities throughout America that live near shipping lanes and next to ports will see clean air benefits.”

The new paper, Impact of Fuel Quality Regulation and Speed Reductions on Shipping Emissions: Implications for Climate and Air Quality, is available at the Environmental Science & Technology website. Lack’s 28 co-authors are from 10 research institutions from both the U.S. and Canada.

Also refer to MARPOL Annex VI - Prevention of Air Pollution from Ships

Needless to say that research and changes in regulations and shipping design are already in the works. Changes won’t take place overnight and care must be taken to work within the existing economic and transportation network across the globe.