I agree to most of your points. In that regard we are thinking along similar lines. However, one small correction.
IAEA safeguards do recognise that India has a nuclear programme outside the civil nuclear programme. In fact this is what Kakodkar should have also brought up when asked about Nuclear weapon status.
This mention is made in the preamble of the document (page 3 of 29 in the PDF available on Rediff site):
Noting the relevance for this Agreement of the understandings between India and the United States of America expressed in the India-U.S. Joint Statement of 18 July 2005, in which India, inter alia, has stated its willingness: - To identify and separate its civilian and military nuclear facilities and programmes in a phased manner;
I understand your point that this is a very oblique reference quoting from a bilateral agreement signed 3 years ago between India and USA,... :-)
Nevertheless the mention about India's military programme is there -- for whatever it is worth.. ;-)