I have reached Yuki nirvana
I don't think that would be a reason? It's not like it was an original story. The first episode adapted the manga shot4panel and is the entire adult murder set-up as well as the children twist. The anime production adapted the entirety of the manga (slight changes to the end or not) - even if Kajiura for some reason did not have access to the at the time unreleased ending, she still would've had most of the story out there.My guess is that she wrote the trailer music going off the first few episodes of the anime, when it seemed like an intimate story about 2 children connecting in the face of adversity. When they handed her the rest of the story, she probably switched gears and adjusted the ost to be more climactic and foreboding.
I figure the original TVCM was created before the scheduled recording sessions and Kajiura just cooked something up with the soloists easier/faster. Or like you said in the last part, Kajiura/Iwanami simply decided later on that it was not a good fit for them and the show.
Regardless, too bad for us. Curse them for not including it as a bonus track on OST. ;P