For me the logical procedure would be to contact the MiKTeX maintainer and ask him if he can integrate the Xindy binaries into the distribution. Everything else seems only half-baked to me. And the more users ask for this feature, the more likely it is that he will do that.
LaTeX forum ⇒ MakeIndex, Nomenclature, Glossaries and Acronyms ⇒ Xindy for MiKTeX
Information and discussion about MakeIndex - the tool to generate subject indices for LaTeX documents.
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