Gene - you're absolutely right about changing the menu and breaking the child themes.
xxxevilgrinxxx -
My first statement ('No') was based on a very early version of the new menu that did not create a default menu. The current version will create one.
As soon as the WP 3.0 moves to beta status, we should be able to present some code to implement the new menu to a child theme. But even this will be for internal use only as long as WP 3.0 is not final.
Following Ptah and his last statement on his blog, I cannot recommend to implement the new functionality into a public child theme or to discuss the integration.
I can guarantee that we will have at least a best practice guide for you as soon as WP 3.0 is released.
Chris