I've been struggling with this whole conversation, and this thread has been very useful to me in trying to figure it out. I agree that Henry is combining irony about Isabella with a secret conversation with Eleanor about Catherine. But the whole interchange that precedes the compassionate comments that you mention here bothers me. I'm having a hard time hearing anything but mean sarcasm in Henry's words:

“You think it is all for ambition, then? And, upon my word, there are some things that seem very like it. I cannot forget that, when she first knew what my father would do for them, she seemed quite disappointed that it was not more. I never was so deceived in anyone’s character in my life before.”

“Among all the great variety that you have known and studied.” - This just strikes me as mean.

“My own disappointment and loss in her is very great; but, as for poor James, I suppose he will hardly ever recover it.”

“Your brother is certainly very much to be pitied at present; but we must not, in our concern for his sufferings, undervalue yours. You feel, I suppose, that in losing Isabella, you lose half yourself: you feel a void in your heart which nothing else can occupy. Society is becoming irksome; and as for the amusements in which you were wont to share at Bath, the very idea of them without her is abhorrent. You would not, for instance, now go to a ball for the world. You feel that you have no longer any friend to whom you can speak with unreserve, on whose regard you can place dependence, or whose counsel, in any difficulty, you could rely on. You feel all this?”

The stuff in bold in this last paragraph strikes me as Isabella-like over-the-top. I feel like either Henry is mocking Catherine, or he doesn't understand her very well to ascribe such extreme reactions to her. On the other hand, I certainly see compassion in Henry's actions - he gives her privacy when he sees that she's upset, for instance, and doesn't push her into talking before she's ready to (I especially like, "I am sorry,” said Henry, closing the book he had just opened;" - he's trying to act like he's not just sitting there staring at her while she cries). But some of the words just don't sound that compassionate to me.