One of the posters here created a script that adjusts the overclocking profile based on battery level and temperature. I don't much like it because once you have worked out the optimal voltage profile for your device you shouldn't need to change it, thus this script is a sub-optimal way of running, but it can be used as an example of how to change overclocking settings based on temperature. If you are interested here is the relevant thread.

Alternatively, do you really need to be running @1200MHz when you aren't using it? If not then there is a guide on the wiki of how to change the clock speed when your N900 is locked/unlocked which will prevent "pants on fire" problems, and when you are using it you should be able to feel it getting too hot and rectify the situation manually.