Cinema Tools does actually resample the audio to about 46khz when going 25 to 23.976. (Check in QT)
Here’s another option using Soundtrack Pro:
1. Open the 25p footage in Cinema Tools and conform to 23.976 (This is destructive process)
2. Open this same file in Soundtrack and Process/Resample the audio to 48000. Save to aiff 16 bit
3. Open conformed movie in QT Pro and delete the audio track.
4. Open the audio saved from Soundtrack Pro and copy track
5. Paste into video movie (OPT+Apple+V)
Video should be 23.976 and audio 48khz