Meh, this is overblown.
They seized the control servers of the malware operation, used that to send an update destroying the bots, after getting a warrant to do so. In the article it makes it seem like they searched everyone's computer, even though the warrant explicitly forbade them from doing so, saw the bot software and then targeted them. This is not the case.
The warrant explicitly forbade the FBI from searching the computers they for the warrant for. The article implies that they could violate the warrant if they want to. And they could. But by that logic any warrant can be abused, let's just get rid of warrants. And the issue at hand, that the court issued the warrant, is being glossed over on this point. The FBI had this capability, they'll abuse it warrant or no if they're trying to abuse it. The warrant makes no difference. So why even bring up the warrant?