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I'm a little confused why your CPU usage would go so high. A hacker, hacking files and uploading rogue files, fine. Usually they just put a file deep in the folder structure and it is some type of malware.
High CPU usage may want to check the database that stores all the comments. You likely have approve comments manually set, so spammers will just keep leaving comments which all get saved in a database. When this database gets too big, it will bring the entire server to a screeching halt because every comment left by spammer actually calls the entire database each time.
Fix is to delete every single comment out, stop any ability for anyone to leave a comment.
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