No, but it will be reset. So the war itself doesn't count in any manner. However, it will take time for them to reset everything and that will inevitably have some impact on matchmaking for next war. Check the main thread for answers from Kabam Miike.
EDIT - My advice for those on the cusp between 2 tiers, fight full swing. It could shift your points next war. Which direction inevitably will hinge on the outcome of the war.
DabNation1
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https://forums.playcontestofchampions.com/en/discussion/185366/alliance-war-ending-issues-merged-thread-title-edited-for-clarity#latest
EDIT - My advice for those on the cusp between 2 tiers, fight full swing. It could shift your points next war. Which direction inevitably will hinge on the outcome of the war.