This looks to me as a bug in a debian specific patch; see 
debian/patches/gdbinit-ownership.patch
+         warning ("not using untrusted file \"%s\"", file);
+         fclose (stream);
+         do_cleanups (old_cleanups);
+         return;

As far as I can tell from the weird cleanup system, the do_cleanups is 
fclose'ing stream as well, and that's why it fails.
commenting out the fclose(stream) there makes it work for me, and the fd is 
closed according to /proc/*/fd


** Changed in: gdb (Ubuntu)
       Status: Confirmed => Triaged

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https://bugs.launchpad.net/bugs/1069897

Title:
  gdb crashes on startup if run as root via sudo and ~/.gdbinit exists

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