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I don't see a good 'n easy way to fix the issue. close() is called in
too many places and I don't wanna add more checks in Python code. 
This patch reduces the mass of warnings to one, but it also changes the
semantic of close() a bit. However it seems logical to set the fd
attribute of the file object to -1 (meaning closed).
Index: Modules/_fileio.c
===================================================================
--- Modules/_fileio.c (Revision 67068)
+++ Modules/_fileio.c (Arbeitskopie)
@@ -60,7 +60,8 @@
 static PyObject *
 fileio_close(PyFileIOObject *self)
 {
- if (!self->closefd) {
+ if (!self->closefd && self->fd >= 0) {
+ self->fd = -1;
 if (PyErr_WarnEx(PyExc_RuntimeWarning,
 "Trying to close unclosable fd!", 3) < 0) {
 return NULL;