Does Windows have a patch for this too? Or just disabling HT is the safest option?
However, looking at the microcode update driver on an updated Windows 10 as of right now, I don't see a recent enough microcode version to fix it. The latest updates appear to be from 2015.
Loading the microcode is straightforward---all you need to do is put a few values in the appropriate MSRs. This is described in the Intel manuals, Volume 3. The microcode itself is embedded in the above DLLs, as a big binary table. The latest entry I see is 20150812 for the Intel 0x40651, aka Haswell.