Remove vm includes in Python bindings that violate layering (#10135)

We don't build these with Bazel in OSS, so we don't have the layering
check to catch these issues, but this came up when importing into
Google's monorepo.
diff --git a/runtime/bindings/python/py_module.cc b/runtime/bindings/python/py_module.cc
index 37bf892..339e508 100644
--- a/runtime/bindings/python/py_module.cc
+++ b/runtime/bindings/python/py_module.cc
@@ -9,7 +9,6 @@
 #include <string_view>
 
 #include "./vm.h"
-#include "iree/vm/native_module.h"
 
 namespace iree::python {
 
diff --git a/runtime/bindings/python/vm.h b/runtime/bindings/python/vm.h
index 202e221..534a66e 100644
--- a/runtime/bindings/python/vm.h
+++ b/runtime/bindings/python/vm.h
@@ -14,7 +14,6 @@
 #include "iree/base/api.h"
 #include "iree/vm/api.h"
 #include "iree/vm/bytecode_module.h"
-#include "iree/vm/ref.h"
 
 namespace iree {
 namespace python {