I have exactly this same question with a slight bend. 

I am allowing some users to create a post using the RAD editor. The link properties page exposes a control that allows the user to see the entire directory structure. I was able to remove the document manager using the HTML editor configuration, but I don't see how to eliminate the document manager or restrict the document manager function from the hyperlink manager page. 

I just tried it here on dotnetnuke, and the document manager function in the hyperlink manager causes the page to spin for at least a few minutes before I gave up. 

So the two point question: 

1) Is there a way to set the root directory for the document manager? 

2) Is there a way to just disable the document manager from the hyperlink manager control? 

Thanks

Kevin