I believe it has to do with the following passage.
The real battle was inside of her—her strength of will against
her own well-founded fears. Even if I did ride in on a white horse
to save her, it would mean only that she would be forced to
question her own strength and integrity thereafter, and that
would be nothing more than a slow death of her self-reliance
and strength of will.
It was something I could not save her from.
And I had asked her to face it.
And I believe it means...
Harry had already guessed that Raith was neutered. But he also knew that Raith still had power to some extent. And he asked Murphy to jeopardize her freedom by facing Raith, who could manipulate Murphy.
Remember that Murphy doesn't like that, after her experience with the Nightmare. It took her years to recover from that violation.
And Harry asked her to go toe-to-toe with someone much worse.