The Supreme Court of India reasonably intervened to reinstate CBI Director back into his position just to facilitate for his ouster as properly done. He was duly ousted after one day by a vote of Justice Arjan Kumar Sikri as the delegate of the Chief Justice of India along with the vote of the Prime Minister of India within the authorised panel for doing that.
CBI is not the only institution in India but there are several other institutions also and all those together (including CBI as well) make the system that runs the Republic of India.
CBI Director Alok Varma’s defiance by resignation for not joining as the Director General of Fire Services, Civil Defence & Home Guards, established further that the system was right in its appropriation about him. He was of no further use in compliance. Although he too is free to take the political path if he likes.
Above all the Prime Minister of India is politically mandated to run the government of India until defeated by a vote of confidence in Lok Sabha or by next general elections of Lok Sabha. Till then the Union Cabinet is a manifestation of his political choices and due to that the whole government of India duly remaines his domain.
Long before Rajiv Gandhi publicly told the press upon a confusion caused by the Secretary of External Affairs in India that they would soon be seeing a new one. Despite all the historic hue and cry then too the Prime Minister of India was politically correct with his that statement.