As far as Indian Democracy is concerned, the learned and visionary people who drafted the Indian constitution, denoted separate powers to three authority pillars, The President of India, The Prime Minister of India, and The Chief Justice of India.
The arrangements in the constitution have for each head of the democracy pillar and none a right to override the authority of other constitutional posts.
As far as PM is questioning the SC judgment, well, yes the govt has always a legal remedy available to ask the SC to review its decision through a review petition.
If the SC sticks to its decision, which is against the govt opinion and understanding, the Govt can always go to the President to ask the President to issue a presidential reference to the Supreme Court seeking a thorough and detailed explanation for the basis of the ruling.
Not only the PM can question the SC order, but also can overrule issuing the Ordinance and get it passed in the parliament.
As long as I remember, last it was Rajiv Gandhi who overruled the SC decision through an ordinance in 1989 in the Shah Bano Case.
Usually, govt do not indulge in any kind of confrontation with the judiciary, but this is just a tradition, there are no such rules.
Let me stretch it to the extreme by saying that the govt can impinge on the CJI if the president approves the action.