Good question and we need to think about it. Lets see what is the strategic responsibilities of the PM apart from leading the executive branch of the Government of India,
1) Prime Minister heads the armed forces through National Security Adviser.
2) Only Prime Minister has the authority to order nuclear strikes.
3) RAW directly works under Prime Minister's Office (PMO). Joint Intelligence Committee as well as IB and
MI also reports to the Prime Minister. 4) Department of Atomic Energy directly works under PMO.
5) Department of Space directly works under PMO.
Now see,
1) So PM holds all the key power in Govt of India but the structure is distributed. So we are depending a lot on one person. Now in foreseeable future no one except Congress and BJP will get PMO. But if we have these key elements of power under JPC than there must be members from Karat's CPM, Mamta's TMC, Jayalalitha's AIADMK etc etc. Now think what will happen to these institutions if they come under such people all the time, except few days of Desai and Gujral!!!
2) There are minimum chances that people from different political parties will agree on anything.
3) They will publicly criticize and blame each other for decisions or failures.
4) There is high probability that a member can be a foreign mole.
Its true that Desai and Gujral were the worst period of RAW but do you want to see them all the time like that? No. RAW has regained most of its capabilities. Don't know about HUMINT but their organisational structure is good now and above all tremendous improvement in the area of technology. So its better to have RAW under PMO just like other key institutions.