I think what you're looking for is this line (around line #947):
$lastmailinfo = get_user_preferences('assignment_mailinfo', 1) ? 'checked="checked"' : '';
in mod/assignment/lib.php, change the "1" to "0", this will default the option to "not checked" UNLESS there's a row in the mdl_user_preferences table for the logged in user that dictates otherwise, a value of "1" for example.