Unlike compromised home PCs, there really is no excuse for compromised web servers.
The vast majority of web servers are managed by someone who is paid to do it, and therefore should be responsible and competent enough to either stop the compromise in the first place, or be able to detect and remove any malicious software if an infection occurs.
If a server is identified as one of the sources of a DDoS attack then it's owner / operator should be notified, and sanctions applied if it's not fixed.