Permanently disable hyperthreading

I am a software engineer with a startup that makes a mathematical optimization system (linear and integer programming). Our software is already multi-threaded, and it runs much faster when hyperthreading is disabled. This is true on all platforms we've tested, including the 2009 'Nehalem' Mac Pro.
In OS X, I know you can temporarily disable hyperthreading through the Processor preference pane, as well as through the hwprefs command in Terminal. However, hyperthreading is turned back on if you resume from Sleep or reboot OS X. And worse, I cannot figure out how to disable hyperthreading if I boot into the 64-bit kernel.
Bottom line: is there a permanent way to disable hyperthreading on the 2009 Nehalem Mac Pro? On a Windows or Linux system, I know that I can disable hyperthreading in the BIOS; I'm looking for something equivalent for a Mac Pro. Thanks.

You're aware though of how effective CUDA is for compilers, computational and scientific and anything parallel I would assume.
I constantly hear about linux performance being better, and I think Windows 7 has eliminated a lot of issues and better optimized.
And then, software development 101 is here:
http://discussions.apple.com/forum.jspa?forumID=728
Intel works closely with, and has updated their compiler libraries but then it takes time to actually learn how to use, and I often get the feeling developers are being pulled away to work on the latest iGadget and iOS and a really optimized Mac OS X for Nehalem etc once Snow Leopard is put to bed - is further out and lower on priority.

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Thanks Carolyn,
I am attaching a screenshot here for you to see that this setting was already set to what you suggested. I didn't need to change it as it was like this even before I post this message.
So the problem still presists and unfortunately your suggestion is not a solution to this probelm.
Last night I did more reseach and found a discussion in Adobe website, it seems a lot of other people have the same issue, and even started a discussion in Adobe website about it. But unfortunately Adobe refuses to address it and enable the end user at least to have an option to turn this message off from displaying permanently on his/her computer.
I am writing down the url links for the two posts regarding this issue on Adobe's website:
Link #1: http://forums.adobe.com/thread/921270
Link #2: https://bugbase.adobe.com/index.cfm?event=bug&id=3058752
Hopefully more people will get involved and ultimately we will either get Adobe's attention, or someone will find a "hack" and post it here for all of us. I have found some suggested "hacks" for Windows environment (you can simply google it, I am sure you will find them too). But so far I haven't seen anything for Mac's Safari browser.
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Permanently disable hyperthreading

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