If you detach the page from the template in dreamweaver you can remove the menu. To detach a page from a template, you would go to the Modify->Templates->Detach from template menu. This would make the whole page writable, but modifying the template wouldn't affect the page. When you edit the main.dwt, does Dreamweaver ask you if you want to update all the pages? That is how it updates the pages if a template is applied to them. You could also edit it using a regular text editor like notepad and remove the menu there.
If you've made edits to the main.dwt, you can also apply the template to the page and the updates should be made on it.