My solution was to search here found some advice on using coolbook to reduce the HEAT and it worked, found a post last week mentioning the Thermal paste issue (just like on the rev A macbooks).
Running VMWare with Ubuntu, Win95, and WinXP. No core shutdowns or heat issues with any of them once vmware tools was installed in the VM.
The machine does run a little hotter with the VM going, but I expect a little bit of overhead...
I'm still considering installing coolbook, and fixing up my thermal paste. I am mainly thinking about performance improvements, though. If it helps, great. At worse there would be no change.