I try to put all images into a child theme so I have portability with my designs. I had been using php inserted into the header but that capability is lost in 3.6.7. I suggest that you add a radio control for "Show Logo Image" and other image fields (such as favicon). The radio button would have two values that would allow the designer to choose between get_stylesheet_directory_uri() and get_template_directory_uri().
FYI I am working around these issues by inserting favicons with a filter in my child themes (seems overkill!) and by specifying logos as ../../childthemename/images/logoname.png