Elinor believed that Willoughby had been partly ruined by his circumstances. As others have posted, his 'early independence' had not given him the guidance he needed.

"Her thoughts were silently fixed on the irreparable injury which too early an independence and its consequent habits of idleness, dissipation, and luxury, had made in the mind, the character, the happiness, of a man who, to every advantage of person and talents, united a disposition naturally open and honest, and a feeling, affectionate temper."

Willoughby was naturally an open, honest, affectionate person. But every bad decision he made turns him farther from his true nature. "Each faulty propensity, in leading him to evil, had led him likewise to punishment." She believes that he is truly suffering and being punished to some degree for all his bad decisions, and will suffer "unhappiness of a far more uncurable nature."

She does not excuse his behavior, but believes that he is not heartless. What seems to be most important to both her and Marianne is that he wasn't faking his love for Marianne. Yes, it wasn't strong enough to make him brave and honest, and he still has the sin of abandoning Eliza on his head. Elinor does not acquit him of that.

In many ways, he's like Henry Crawford. He is capable of valuing and loving a woman who would be good for him, but not quite enough. JA cites both men as suffering from 'early independence' and in Henry's case, a 'bad example' (his uncle.)

What really shocks me about Elinor's state of mind is that in the next chapter (45) for a moment, she 'wished Willougby a widower' so that Marianne could be happy, since she doubts Marianne will ever love anyone else. This is shocking to read, but makes me wonder what if? If Mrs. W. died, Mrs. Smith forgave Willoughby, would Marianne make him provide for Eliza and maybe even adopt her baby and raise it as their own as atonement?