Well, as I've only read the manga, I'm not entirely sure I can explain where the anime may have differed, but here goes.
We were basically given to understand that Himiwari was simply born a carrier of bad luck, and that unfortunate things tend to happen to those around her.
I don't know about Watanuki leaving the shop or Yuko coming back; those things didn't happen in the manga...
Himiwari bares Watanuki's scars as a price that she and Domeki paid (Domeki paid in blood) to Yuko to save Watanuki's life after he had fallen out a window due to Himawari's 'bad luck' thing.
They don't end up together, no, but I think the romance is no less compelling or real.