It turns out that you can disable the Fault Tolerant Heap by renaming the DLL that it uses: Windows\AppPatch\AcXtrnal.dll. I had tried this before without success, because on Windows Server 2008 R2, the file belongs to "Trusted Installer", which prevents anyone except an installation program from deleting or renaming the file.
If you go to the advanced options in the file properties, you can take ownership of the file away from Trusted Installer and give it to yourself. Then you can add yourself (or just Administrators) to the list of people with Full Control of the DLL.
And then you can rename it.
This will prevent the Fault Tolerant Heap from running on the system at all, at least until you get an OS update that reinstalls it, at which point you'll have to do all this again.
But -- for the time being, at least! -- the Fault Tolerant Heap has been moved to the correct location.
The trash heap.
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