I'm not sure it would be that easy since I believe e.g. I/O can go through the System process (or other processes even), which has full affinity. We'd likely have to set thread affinities for all processes/threads. But then it would clash with manually-set affinities, and I'm also not sure if it would have worse performance than actually disabling hyper-threading or not.

Right now I'm looking at what making a UEFI application to disable HT before boot might involve... not sure if that's too late in the boot process or not.