Theoretically speaking, the Counter Force shouldn't be so easily subverted. In practice, Alaya is still formerly a chunk of the Planet's will and the Planet is inscrutable at the best of times and actively hostile to humanity at the worst.
She -does- have a personification in the Prisma setting (don't watch that one unless you want to get put on a watchlist, that's the one Chloe, Illya, and Miyu are from) so if she does, it'll be that one. The Prisma timeline distinguishes itself from the other branches by this one being What If Pandora's Box Never Got Opened? Which could be an interesting plot to work with. It's a shame about the Piers Anthony-grade... everything else.