Who leaked info on section 9's kidnapping of Mr. Serano?
Secretary General Yakushima would have feelers out to pick up on any operation like the one Section 9 were pulling off. The universe also doesn't set up the enemies as inert - they are active and have skills - at that level of espionage, the Secretary General would totally have the resources to uncover what Section 9 was doing. 

Interestingly, one of the possibilities is that Aramaki leaked it himself, or left a trail to put the whole death-to-rebirth, process into action. However, it is more likely he just reacted to the situation and any small member of Public Security could have had some type of tap on Section 9.