She knows he's her father who married her exact-lookalike, chased her across half the world, and invaded her homeland after mysteriously surviving a boat ride where her mom died.
He did the same just like any other ruler in the world? (especially Foltest+his sister ya know). Nothing makes him a psycho, a monster or a scumbag. He did it for the state.
Again, Ciri has never seen Emhyr. Well she did, but Emhyr let her go right away (end of Witcher saga). She doesn't know his point of view. He didn't have time to explain it to her.
He is her father - him chasing her around the world is understandable. He wants to see his daughter. (Btw, Geralt did the same)
Also, just got another counterargument concerning Emhyr corrupting Ciri.
1. Ciri doesn't care about gold - you can clearly see it when Emhyr rewards Geralt with gold. Just look at her reaction - she doesn't care about riches. Quite the contrary - she looks down upon Geralt if he accepts gold.
2. When she leaves Emhyr's audience it seems Emhyr told her something that even Geralt doesn't know (again her reaction implies that, (see above - Emhyr's point of view)) - something very important, that made Ciri to make her final decision. Her OWN decision by the way - she isn't a child anymore.
Ciri has royal blood - she gets power as the empress to change the world and make it better place. Who knows maybe she will rule in other way, not like Emhyr does? But that is another story.