Instead of using Boot Camp, run your application in virtual. I do this all the time with SQL Server and MS Visual Studio in Parallels.
In order to use 3D design applications (which the original poster expressed his/her desire to do so), you'll need as much juice from your graphics card as possible (3DsMAX 9 wouldn't run on Fusion, for instance). Unfortunately, Vmware/Parallels are not really efficient with 3D graphics (I am not sure, but I think they only support up to DirectX 7?). Best bet for the OP is boot camp.
I have yet to find any issues with Input Remapper, but whatever the OP decides, please do let us know, help us help others =].
Could this be causing some permanant damage?
It really depends. The Core2Duo chip on MBPs are designed to work normally up to 80C (don't quote me on this though...). Will it cause long term damage? Possibly. Heat makes the internal components expand, and when it cools off, they shrink back to their original size. Now, I'm no trying to scare you or anything, but constant temperature changes can damage your logic board overtime. Do remember: this
is a laptop, as powerful as it might be, it is not advisable for you to use extremely demanding applications on it.