For the readers who haven't waded through the other thread (focusing in no small degree on hyperthreading not the reverse), let me link the Intel paper that probably sheds the greatest light on this subject:
http://www.intel.com/technology/magazine/research/speculative-threading-1205.htm
As to pitfalls, I'm sure there will be plenty, not least the continued encouragement of developer laziness and postponement of threaded design to future compiler + hardware solutions.
However, I don't think that this in itself will be any worse than say a badly written app + OS scheduling that would let such an application "take over" multiple CPU's on a non-reverse-hyperthreading machine. Moreover, not all apps will benefit from this tech and "take over" all CPU's -- just those ones that are built to incorporate this feature during build time.