I don't see any other ending having been appropriate for this episode, as I feel that the eternal battle between the Lazari was crucial to conveying 'The Alternative Factor''s theme of a being who is truly forced to be in a 'literal' state of continual war with oneself (which I would like to think was Don Ingalls' symbolic statement on the ravages of psychiatric conditions such as Multiple Personality Disorder, Bipolar Disorder, et al.). Also, the episode was underpinned by its prolific use of psychedellic visual effects and 'trippy' anti-matter plot point to serve this narrarive message.
No, 'The Alternative Factor' is not a top-tier Star Trek TOS episode, but it does have a number of merits, especially if my thematic interpretation of the episode is at least somewhat accurate.