Excellent analysis. It's a much more grown-up Wonder Girl than we saw even a year ago. I think it began when she basically told both Tim and Kara that she was using both of them to get over Kon (and both of her relationships with them survived) that got her to the place where she is now. And I think you're right she's upset because she thinks it will hurt Kon (her own feelings were resolved many issues ago) and she doesn't want him to be such a great loving guy only to find out his GF was macking with his best friend after he died. It's a sign of Conner's maturity that he understands immediately.
Though it is ironic that the man who created the Tim/Cassie ship (much talked about at the time it was happening) - Geoff Johns - is now the same writer who dismisses it so cavalierly.