Once customers' computers are infected and become part of the botnet, they are unaware of that fact and may not have the technical resources to solve the problem, allowing their computers to be misused indefinitely. Thus, extrajudicial, technical attempts to remedy the problem alone are insufficient and the injury caused to customers continues.
While this might not be the most relevant argument legally (after all, one is generally not allowed to bring suit based on injuries to third parties) from an emotional standpoint, it almost certainly made the judge more likely to grant Microsoft's requested relief.*
In any case, there's too much there to succinctly summarize here. Further, there's no reason to want to read a summary. The information is valuable enough to be worth the time to read in the original.
*Yes, I am aware that harm to third parties can be used to establish that issuing an injunction is in the public interest. However, Microsoft invoked its customers' interests essentially everywhere, not only when arguing that the public interest would be served by granting a TRO.