To be very honest, I don't have answers.. But we will know in the final verdict..
He is directing the JIT very effectively till now. He is literally implementing his verdict. I think what he wanted was that, since SC is not a trial court, it shouldn't disqualify PM without due process. In his verdict, he didn't refer the investigation to institutions, but formed the JIT under SCs supervision.
He picked gems and has sided with them during the whole process till now. He didn't delay the process significantly, despite multiple requests from JIT to give it more time.
Maybe, it was his professional opinion that SC should give a chance to PM because there is no appeal against verdict in 184(3) cases?