Given how supportive and understanding CSS was with LBY going to war for revenge in ep 41, she's obviously not against LBY getting revenge. She has also moved on about the violence, you don't really see her mentioning that since her departure from Hua county.
If we talk about hypocrisy, then so is LBY. He wanted CSS to always share her problem with her (e.g., 5th princess pushing her), yet he won't do the same. The second thing is from the various upcoming preview, she obviously felt that LBY was hiding something, and she asked him over and over again whether he was hiding something from her, giving him opportunities to open up to her.
From what I read earlier, even after he massacred the Ling family, she still hopes they could be together. However, she overheard him telling the Empress that he was willing to give up on her for revenge. The issue is not him hiding his secret, it wasn't even that she was not as important as revenge, but him giving up on her while she continued to hold on to him. She felt betrayed and disappointed, especially since he was the one who led her to fall in love with him, believed him, and gave her the hope that he would never abandon her, yet that is what he ended up doing.
I think it makes perfect sense that CSS is upset with LBY.