My guess is that when MC was installed, it did it's automatic "find all music files" thing after the 45 second countdown and it imported all of your ITunes files.
You could start over again if you don't have anything invested in your setup. Just clear the Library (File > Library > Clear library) and then import the folder you want. But that's probably not a good solution for you.
You can easily delete everything that's in the ITunes folder from MC. Go to the left navigation area and go to Audio > Files .
In this view the first Pane should be "Location" which is the location on disk. Drill down into this pane and find your ITunes folder. Click on it. You should now see all of your ITunes files displayed in the files area at the bottom. Just highlight them all and press delete. Take the default, which is to remove from MC, but keep them on disk. That should do it for you.
Be careful!
Good luck.
Brian.