There is an option to turn comments off already, though. Now it doesn't do what you think it should do (it turns off comments on new posts only). Past that... We can't use an htaccess globally because not everyone is on apache. So there isn't a 'global' solution beyond turning them off. The file has to be public available in order to permit anon comments and ping backs, so you'd have to add an extra wrapper around it when comments are off to say 'And if they're off, auto reject.'
However... That would conflict with membership only setups that DO turn off comments and then use the code for other things :/ So we can't break existing preconceptions. You'd have to use another plugin to override it and turf all comments.
That said, if you've turned off comments, then you can safely delete/spam anything that shows up, right?