The project has its supporters, including the borough president, the Brooklyn Chamber of Commerce, and others. Community Board 6 approved, in its advisory capacity, the zoning change in June; this hearing was before the city's Board of Standards and Appeals, whose job is to provide "relief" from the zoning code to property owners.
The blog reports the plan has its detractors as well:
Quite an impressive number of Gowanus artists, musicians, film makers, lighting designers, jewelers and non-profits... testified against the [Whole Foods] project as well. They argued that there are few industrial manufacturing zones left in the city and those that remain need to be protected. They pointed out that the Gowanus area is not the waste-land Whole Foods depicts it as. Rather it is a vibrant manufacturing and cultural zone that permits growth that can not be sustained anywhere else. As an industrial zone, they pointed out, the Gowanus area is vital for the economic recovery of the city.
Marty Markowitz has made similar remarks about manufacturing, though not in regards to Gowanus specifically.
Read the full report at Pardon Me for Asking.