I can't lose Luke, too

Um. The line was said in the context of the loss of her other parental figure: Jocelyn. Luke is for all intents and purposes her father, and she's understandably scared at the prospect of losing him just like she lost Jocelyn. It's not that hard to comprehend if you'd bother to listen to the context clues.

She cares about Simon, and I'd say she cares about Magnus as well - her being afraid to lose her father doesn't make that any less true.

God are some people really so dense. She was upset after losing her mother and she was terrified that Luke was in danger and that she might lose him like she lost her mother. Hense the "I can't lose Luke too". If Simon had been in danger at that point and not luke clary would have said "I can't lose Simon too". It's not that difficult to understand its just about using your brain.