This whole "running to the ship" reminds me a lot about Usopp situation in end of Water 7 arc.
The difference is, in Usopp's situation, everyone aboard the ship, from Chopper to Zoro to Luffy, was anxious and waiting for him to appear.
Here in Yamatrash's case, Straw Hats genuinely agreed to leave her behind, like an unwanted baggage.