In public perception, the office of the Prime Minister (PM) has been “devalued” to a great extent. It is true that in recent months, the PM has been criticized greatly. Yet, a distinction must be made between an individual incumbent and the institution. The PM is, after all, the head of the government and also has the final say in authorizing the use of nuclear weapons.
If only for that reason, the PM should be kept out of the purview of the Lokpal. There can be other mechanisms to check malfeasance in that high office. For example, once a person demits office, penalties for abuse of power and corruption can attract greater punishment and greatly simplified judicial and evidential procedure. That way not only can a particular individual be punished but others sufficiently deterred.
The last thing India needs at this hour is to weaken an institution that is in need of greater empowerment.