I've run into this issue already, where when the battery is in and I'm running Folding@Home or other extremely CPU intensive tasks a temperature monitor reports temperatures up to 200°F/92°C. Obviously running a laptop that high isn't recommended, but the only fix I could come up with is removing the battery. After that temperature dropped to 158°F/70°C. Note that killing the extremely CPU intensive tasks it dropped the temperature to 120°F/49°C.
My question though is why does having the battery in (not used since its plugged in and 100% charged, just in) cause the temperature to jump so high? Its not even the battery that's hot, its just the area where you plug in the power cord. I'm not sure exactly how the power is wired, but if its going through the battery then how is it that only the power plug is hot and not the battery? Why is the power plug so hot? If its not always charging the battery, then why does the mere existence of the battery spike the temperature?
For reference this laptop is a few month old Lenovo Thinkpad X220 Tablet. Clogging fans aren't an issue as I experienced this issue 2 weeks after receiving it. It has a Sandy Bridge CPU so there's no hot GPU which might cause problems. Unsurprisingly the heat issue is there whether I'm in Fedora Linux or Windows 7.