It's why she leaves to find Shiva when she wants answers, why she ends her series by declaring, "I'm not Batgirl, I'm something else."
See, that doesn't count because I'm not sure I like it. =P
I also don't think she ever really "needed" punishment, but when applying her interpretation of the batcode to herself, she concludes that that is what she deserves. (Which she doesn't, because it wasn't her fault.)
I guess my point is that her interpretation of the bat-code is wrong, because I think the bat-code does include redemption and giving people chances. It's just that Bruce is far less patient with that sort of thing, that he doesn't always take the time to explore the possibility of redemption. If Bruce knew how she'd handled the Alpha thing, I don't think he could've blamed her or disapproved.
The crux of the problem, I suppose, is a lack of communication. Bruce has always just assumed Cass understands his moral code in toto, because of their similarities and shared passion for preventing murder and people getting hurt. And they do actually have the same code, it's just that Bruce doesn't often focus as much on redemption as Cassandra deals with it on a regular basis.
So Cass thinks her mere existence is in conflict with the batcode, when that's not actually what Bruce thinks at all. He knows that even though she's killed, she's still a good person who wants to do good and is capable of doing good, and trusts her to do just that.
Cass isn't there yet with the Batclan, she still sees them for what she wanted from them when they met.
Well, to get picky, Cass isn't really anywhere at the moment.