I'd say the case of the Squadron Supreme was a different case. There, they were trying to establish order and rid themselves of the threat of supervillains in order to establish a utopia.
The JLA here was acting out of a need for self-preservation. They saw that Dr. Light not only violated one of their loved ones, but was very capable of doing it again. It's a much more personal case, regardless of if they did it to others. Unlike the case of the SS, it was mainly to return to the status quo.
