There was a bit of a dilemma in cultivating the Sin of Pride Mark that Eliza had to face.
It made her stand at the crossroads.
Each of Eren's words made sense to Eliza in some way. However, she had started to see Eren as one of her mental blocks in life. His very existence was a threat to her prideful nature. So she had to deny him and his opinions to validate her pride.
And yet, having pride did not mean that Eliza had to be completely dense about how Eren had waited for her to gain her bearing back, even if he had done it to hurt her pride. She decided to pay her due diligence so that Eren's act would not become one of her mental blocks in the future.
"I have to thank you for waiting for me to recover and get back to my senses, Eren," in a rare display of sincerity, Eliza conveyed her gratitude to Eren.
Elize decided to convey her gratitude to Eren so that the incident wouldn't become a blemish on her pride.