And IF we see her again it's going to be when she goes splat when Ashura-ou wakes up. A beautiful moment indeed; It's been far too long since they've given us a violent and bloody death.
Well, we don't really know that Ashura-ou would do anything to Chii. It's a possibility, though. I wouldn't wish it on Chii, particularly considering she hasn't done anything but let herself be turned into an alarm system, but I do miss the bloody violent deaths.
To respond a couple other debate points:
I also don't think it matters that this isn't Chobits - all the past evidence still shows that CLAMP doesn't separate couples. Chii doesn't feel about Fai the same way she felt about Hideki - remember how distressed she would get in Chobits about the idea of being without Hideki, and compare that to how she responds when Fai says he's leaving. She's completely fine with the idea.
Yes, Freya was in love with her creator - but that didn't end well, so I don't think it actually stands in support of Fai/Chii, though I doubt CLAMP would ever be stopped from doing a couple by some taboo -they've done incest, pedophilia, abuse and just general screwed up before. However, they have yet to break the soulmate rule in Tsubasa.
I'm pretty sure that when Fai is looking regretful in the Celes scene, he's not looking at Chii. He's looking past Chii into the water at Ashura-ou. After all, he addresses his next line to Ashura-ou from the same position with the same expression. So, I don't think that was a reaction to changing Chii's form.