In the factory at the end, when the T-1000 pins Sarah to the wall with his needle/finger and tells her "Call to John", why doesn't he just kill her immediately and call John himself (as Sarah)? We saw him do this with John's foster mother earlier in the film. And it's already been established that any subject that he copies is terminated, so there's no point for him to talk to her at all.
Cameron set up the T-1000's rules earlier on (with John's foster parents), so I don't understand why he slipped up here.
Maybe it was because the T-1000 realized that terminating and copying her would not be successful, because of his failed attempt with John's foster parents.
Ther is one error in your point; the Arnold never tells john that the subject is "terminated" for sure. He uses the word "typically." Meaning, killing is not always the outcome.
The novel said that the T-1000's vocals had been damaged by the nitrogen bath. It is possible that it put the Terminator's foiling the attempt with the foster parents down to John's astuteness. Others have suggested that it had some malevolence, so wished for Sarah to be the one to betray her son.