Well for starters, Haku is voiced by Miyu Irino (same as Sora) so there's a connection right there. (^_^
More seriously though, I like to look at themes between two properties and see where they link up to see how compatible they are together. Spirited away is mostly about a girl essentially learning how to grow up, and how to gain the courage to take on future challenges in life. In her case, surviving a big move and leaving her friends behind while learning how to stand up for who she is and what she believes in.
I think this could definitely be connected to with Kingdom Hearts, especially with the theme of "our friends and memories are always with us, even if we aren't physically together". Believing that, in a sense, gives one courage to press on through life knowing you aren't alone.
That being said, it would be a bit difficult to work that into a world, I think, because Chihiro mostly had to learn how to stand up on her own. It wouldn't really work if Sora was there kind of doing everything for her, haha. Though, they could relegate him to a funky assistant role and have SDG replace the little rat and bird thing that follow her around. However, if the story was more expanded and focused instead on a character like Haku or one of the witches (even Kaonashi) I feel like that could be a pretty interesting experience.