Pretty much every such product uses libz, libssl, and these days websocket and javascript libraries. Are they malware? Very often the border between malware and non-malware is not clear. There are many command and control software that have no payload, and no exploits to spread. Are those malware? What about IRC/XMPP servers, webRTC/STUN/servers + proprietary equivalents, name resolution services (from DNS to some company's active directory), DHT, game servers (minecraft, quake) and other public services that often serve as or contribute to command-and-control hubs?
But I'm not really interested in drawing an actual clear line. I'm worried especially what will happen if a local police officer or court judge takes action based on their personal assessment of a cybercrime. And now, with this law, international action. Right now often DNS is sabotaged, usually on a way larger scale than necessary, to achieve a court order. Inconveniencing everyone, often right up to gTLDs.
Usually such a court order then doesn't work because the fact that a court case exists (and the time these things take) serves as ample warning for the malware authors plus you can use encryption to hide the command and control servers beyond the reach of even sabotaging DNS. And even that is assuming the damage isn't completely done by the time a decision is reached.
Actual prevention of malware attacks is the domain of extra-judicial agents working at security companies, and they usually disable malware by injecting their own payloads, something that even currently is highly illegal, and sometimes causes the justice system to go after these individuals.