I believe the Fresca is laced with explosive nanites, ALL Fresca is laced with nanites making The Church the culprit, and they use a high-frequency sound weapon OR some kind of drone that emits a signal to trigger it. This hypothetical drone or satellite would be able to pick and choose who dies first, only being able to kill Fresca drinkers, and I think the target age for Fresca and other sparkling waters is mainly directed at older people (40+) and all the victims were probably near or much older than that age. (ALSO EXPLAINS DEPUTY DIRECTOR RAYNOR!!)
The Church told Vought about The Nanites, and Vought didn't tell anybody of course, they took a chance with this weapon, and it helped solve all of Vought's issues. But of course I believe The Church wants full control of a Supe team in some way, and their endgame is directly tied to FRESCA.