There is a third party app - Launchpadmanager available here.
And yes i do understand what you are saying about the current setup as by default it includes all those loverly Utilities (Terminal/Activity Monitor/Key Chain/ Disk Utility etc... that live in the Utilities folder within your Aplications folder.
Probably not the best on business User machine !
On a user machine it would be better if you had the abllity to disable lauchpad completely.
The short answer is that there is no way to use the LaunchPad this way currently. I completely agree that the launch pad should work that way - customizable.
Anyway, the best solution I've found is to make a folder/group in the LaunchPad called "Not Used" or something and drag what you don't want cluttering up your LaunchPad into there. That way it is out of the way but not deleted off of the computer. Hope that helps.