How in the world does that not constitute murder?

Any plans Kirk had prior to his "original" being dematerialized are still equally likely to be carried out by the "copy" Kirk, any preferences he had will still be defended, and so on. Nothing of consequence seems to have been lost; an observer unaware of this little drama will notice nothing different from what he would have predicted, had Kirk traveled by more conventional means.

To say that a murder has been committed seems like a strained interpretation of the facts. There's a difference between burning of the Library of Alexandria and destroying your hard drive when you have a backup.

Currently, murder and information-theoretic murder coincide, for the same reasons that death and information-theoretic death coincide. When that is no longer the case, the distinction will become more salient.