Quick experiment with Visual Studio 2005 shows that you can enclose those headers in your own named namespace and then use what you need from this namespace (but don't use the whole namespace, as it will introduces the namespace you want to hide.
You may be stuck using explicit namespaces on conflicts:
string x; // Doesn't work due to conflicting declarations
::string y; // use the class from the global namespace
std::string z; // use the string class from the std namespace
...then the effects of any using directives within that header are neutralized.
That might be problematic in some cases. That's why every C++ style guide strongly recommends not putting a "using namespace" directive in a header file.
How about using sed, perl or some other command-line tool as part of your build process to modify the generated headers after they are generated but before they are used?
For future reference : since the XE version there is a new value that you can #define to avoid the dreaded using namespace System; int the include : DELPHIHEADER_NO_IMPLICIT_NAMESPACE_USE