EXCELLENT point! I think I may put it in my headcanon that Picard decided not to destroy the Borg because of a lingering bit of Borg presence in his system that Dr. Crusher couldn't detect. (Which would also conveniently foreshadow Picard still having a bit of a Borg connection in First Contact.)Even worse is that you would think Starfleet would have suspicions about Picard's lingering mental state/PTSD or even his loyalty to the Federation after the Wolf 359 massacre. You have a former Borg leader who just decided to NOT DESTROY THE BORG. How does this go unchecked? I'd imagine the blowback would have been catastrophic.
But yeah, Starfleet investigating Picard for his decision in "I, Borg" makes all the sense in the world.