Honestly, I could see why Disney would be hesitant to let Sora into Smash.
From a brand perspective, joining Smash is a lot more risky than you might think. You're essentially signing up your character for a game where they shoot at, slice up, and use a hammer to beat a plethora of other characters for sport. Obviously, it's done in a relatively slapstick way, but that could still be a step in a slightly more edgy direction for many of these characters' brands. Likewise, you also have to accept that your character is appearing alongside any characters in the game or any characters that will be added through DLC in the future. It's not enough to be cool with your character sharing a product with brands like Metal Gear, Persona, and Bayonetta, you have to be cool with the possibility that series like Resident Evil and Doom could be alongside your character next.
Contrast this with Disney, a company that has made excessive brand control a major pillar of their business strategy. If Disney licenses their characters, they want to be as hands on as possible to ensure you're using their characters in a way that's consistent with a very particular image. Step outside their set lines? Congrats! You've just earned your product a spot in the "Forget this ever happened" corner of the Disney vault.
Despite Kingdom Hearts being aimed at an older audience, we've seen Disney apply this approach for this brand as well. And, I mean, why wouldn't they? Not only has this approach worked in the past, but Kingdom Hearts is also connected to numerous other products Disney places a lot of value in (Mickey Mouse, their animated library, Pixar's catalog), so controversy involving Kingdom Hearts could ripple out and effect some of the big money makers. So, when its framed like this, why would you take that risk? Pleasing a handful of fans and getting some free publicity and royalties really isn't worth putting someone else in the driver's seat when you've got a very specific destination in mind.
That being said, I do feel sorry for Sora's fans. It always sucks to take a big blow to your chances, no matter who the character is. I have no real connection to the character myself, but I do have an old friend who absolutely loves the series, so I would've been interested in seeing Sora for her sake.
On a side note, it's almost a miracle that the Pokemon Company is still onboard with Smash, considering how protective they are of their brand. It wouldn't surprise me if they wanted off Mr. Sakurai's Wild Ride in the past, only to get rangled back in.