If I understand your question correctly, you are asking if USGBC allows its LEED-certified buildings to have air conditioning. The answer is yes.
CFC (Chlorofluorocarbon-based) refrigerants must not be used in new buildings and must be phased out of old ones. This was the standard refrigerant used for years in the industry. Now, thanks to the pressure of greening the industry, new more efficient refrigerants, free of chlorine and non-ozone depleting, are readily available.
CFCs not only deplete the ozone layer but also absorb outgoing infrared radiation from the earth, thereby increasing greenhouse gases. Hydrofluorocarbons (HFCs) are better but still not the best solution. They do not deplete the ozone layer but they still cause greenhouse gases. New products are now on the market that use C02, ammonia and even water. As one might expect, the latter is our best shot at a perfect refrigerant.
Other related issues with air-conditioning are the system's efficiency, noted by its SEER rating, and indoor air quality. There are ways to avoid air-conditioning altogether, especially in new buildings, by using designed passive ventilation techniques to cool air. Active systems using PV, geothermal and heat pumps can also help avoid air-conditioning.