This was clearly a large-scale coordinated effort spanning multiple countries, multiple organizations within the US including DOJ lawyers, named and unnamed industry partners, etc. This is not a context in which a single group could do unethical clandestine things without the knowledge and buy-in of other parties, nor would it be something the FBI team working this case would have any incentive to do. They were tasked with dismantling this botnet and removing the malware from victim machines, and that is what they did.