If Blizzard decided, for example, to go after keyclone and outlaw multiboxing, wouldn't they have to ask him to stop first? Wouldn't taking him to court based on what his program has been used for prior to Blizzard deciding they don't want it be the same as a law taking effect ex post facto, which can't happen?

However, if Blizzard decide to start banning accounts instead of taking legal action, they have every right to do this. According to the EULA, your account and characters are the property of Blizzard, and you can be banned at any time for any reason, at Blizzard's discretion.