It is excruciatingly painful to deeply customize WordPress load process.
It’s not quite clear if your requirements here are performance related or tied to soemthing else.
For your question as stated there would be about following approaches (madness ascending):
- get rid of actual code causing unwanted queries, altogether or via techniques like caching
- customize the load process in runtime, such as using mu-plugin to control which plugins are loaded
- build a custom SHORTINIT endpoint and load the required minimum of WP core in “manual” way with your own code
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