Two of the three (current) top-level replies compare BSDs to Linux in general, but that really has nothing to do with whether you disable HT. Using Linux should not have stopped anyone from listening to Theo and disabling HT months ago. Your security authorities don't have to be your kernel developers.
What about everyone else? Many companies only operate a handful of servers, and they often don't have the staff to know the kernel that intimately, so they rely on sane defaults. These companies are also not typically using their CPUs to the max, so disabling HT seems like a reasonable default.
If you know enough to know whether up should be using HT, you can enable it yourself.
In fact, cache p3 timing attack was known as "theoretically possible" back in nineties, but was booed out of the conversation by "big name security analysts"
If that's true, it's wonderful and I applaud them for making this decision.
I haven't been following this conversation closely; is there any serious change of Linux (some distributions, or the kernel upstream) disabling HT by default?