Warlord --- Well the music is certainly edited. It fades out as Kirk says, "She took it" -- at least it does on the 2 episode DVD copy that I took a clip from as reference. Wouldn't shock me to know that the audio is slightly off on this disc. What version of this episode are you using?
I think it goes like this:
MCCOY: No. That incredible Vulcan physique hung on until the life-support cycle took over. His body lives. The autonomic functions continue. But there is no mind.
KIRK: That girl.
[Start the cue]
MCCOY: What girl?
KIRK: From that ship. She took it. [Cue fades] I don't know why, or where, but she must have taken it. Bones, how long can you keep him functioning?
* I relistened several times, and I think you are correct. The version of this cue as used in this scene is not on on the disc. Track 17's cue plays earlier. However, I can still hear the same motif in the ending of the cue as Kirk speaks and it fades, so I presume it is indeed from Spock's Brain -- I "think" (stressing I am only thinking, not knowing for certain) it should be on Track 18 on the Soundtrack, but is missing -- It should be "NO MIND" although it says it is on the CD, it isn't. Track 18 starts with "Tense Moment" instead.