So will this be affecting most Macbook Pros of the past few years? If so, there's a way to disable hyper-threading, but you need Xcode (Instruments). Open Instruments. Go to Preferences. Choose 'CPU'. Uncheck "Hardware Multi-Threading". Rebooting will reset it.
This is kind of like cutting off your leg because of a hangnail. I've been running a Skylake MBP for more than 6 months for compilation workloads and haven't seen a single processor hang. I'm much more annoyed by the completely unpredictable desktop assignment on monitors when hotplugging DisplayPort connections on multiple displays. This one bothers me every day.
What I see:
Same monitor/monitors plugged into same ports produce consistent configs.
I get a unique config per monitor/port.