While I am quite certain Catherine de Medici was one of the organisers of the Massacre, I don't think there is enough evidence to suggest she specifically targeted Coligny. From where I stand, Duke de Guise had far stronger motive for he blamed the Admiral for the death of his gather.
In regards to the marriage and subsequent massacre, although Marguerite was forced to marry Henry of Navarre (according to rumours, she was in love with the Duke de Guise, who returned the feelings and hoped to marry her), she did her best to save Henry and many prominent Huguenots. It is said that she hid them in her chambers, and refused to open the doors and give them to the Catholics for slaughter. It was Marguerite's sister Elisabeth who had alerted her of the impeding massacre - against Catherine's explicit orders.
I really wish this union resulted in a child: their boy would have been an undisputed Heir and quite possibly, the civil war would have been avoided. Granted, women could not pass rights to their children, but Marguerite's son would have been the grandson of Henry II and nephew of Francois II, Charles IX and Henry III (and of course, the son of Henry of Navarre as well) - pretty good credentials. The existence of a son with Marguerite Valois would have helped Henry IV's cause no end.
Of course, what with their acrimonious relationship, virtually separate lives, multiply mutual adulteries, and even assassination attempts, siring a child was never a strong possibility.
Mind you, Henry and Marguerite became pretty good friends later in their lives and, according to one historian, Marguerite and Louis XIII were among the few who shed genuine tears for the assassinated Henry IV.