First, anti-malware tools (like MSE) don't wait until after the infection occurs. For a piece of malware ot infect something (lets say you open an email with a trojan or some other malware), before anything happens, the tool scans the email. The malicious code doesn't have a chance to run before it is scanned. Now, to detect the malware, it does rely on definitions which come from previously seen malware.
FIM and HIDS on the other hand do wait until after the infection and then tells you about it later.
Now McAfee has a tool (and I cant' think of the name... Artimus maybe) that instead of relying on definitions, looks at what the code is going to do and tries to determine from there if its malware. For example it might let an executable designed to update core components of Windows run if the code is signed by MS, but if there's no signature, it would prevent it. However, its certainly not free.
As for the article you linked, its not talking about the casual web surfer. Its talking about advanced adversaries with resources behind them and more or less directed attacks. Anti-malware tools like MSE are going to be relatively useless in these situations.