It seems to me that if the Court wants to intervene in this question it makes sense from the Court’s perspective to play a strategic waiting game. The BJP-led government came in with a large electoral victory and one of its first major legislative achievements was passing the 121st amendment. In this context, it would have been quite hard in August to strike or read down the amendment even if the Court had thought that the question was ripe then.
Going forward, the Court is a bit more constrained in terms of timing. As soon as the amendment becomes part of the Constitution the question should become ripe and the Court will have to decide whether or not to hear these PILs (or challenges similar to them). It is hard to imagine letting the Commission function for say five years and then suddenly accepting a challenge that the Commission violates the Basic Structure of the Indian Constitution. However, the Court could accept these petitions for hearing and then sit on them waiting to see how the Commission plays out in practice or for a more opportune time. Of course, just because the Court decides the Commission does not violate the BSD does not mean that it could not find other grounds to intervene in its functioning down the road, particularly if it thought members of the Commission were overreaching their mandate and undermining judicial independence.
This government has made clear that it believes it should be more involved in judicial appointments and that the unaccountable, opaque, and much criticized collegium system should end. The Supreme Court, on the other hand, has a long track record of protecting the judicial appointments process from what it views as poisonous political meddling. It would be surprising if the 121st amendment ended this conflict once and for all, but the judiciary might be slow to make the next move.