ana-answers:

I would argue that you’re misinterpreting the scene. Carmilla is basically saying that staying innocent is all well and good for trying to save the world, but that you cannot expect to save the world and stay innocent. Laura’s lost that in killing Vordenberg. She killed a man to commit a selfish act. Carmilla killed her mother and risked her soul to commit a selfish act. To save the person she loved.

I guess you could say, if anything, they are becoming more similar. 

Carmilla might not have wanted Laura to lose her innocence, because she values the beauty of that innocence. But she’s also a realist, and knows that Laura could never hope to get through this unscathed. 

They’re moving forward. Together. Towards a point where they can see eye to eye on things that they previously disagreed upon. Laura’s realized she cannot change Carmilla, and Carmilla’s realized just how far Laura cares for her, and how far she’ll go to keep her safe.