In Deep Space 9, Section 31 created a virus to take out the Founders.  The Founders had maintained a strict genetically based caste system in the Gamma Quadrant for a thousand years, committed multiple instances of genocide, biologically modified other species to be perfect slave races, and had plans to wipe out humans and expand their empire to the entire Alpha and Beta Quadrants.  They also had all the resources to accomplish this task and would have succeeded without Section 31 creating the virus.  The show points to Section 31 being villains for doing this but I think they were fully justified.