I used to have an Acer Netbook, which would, regularly overheat, if I dared use it, more than a 1/2 hour at a time, with the "on-board" Hard Drive.
HOWEVER, I had no trouble, running Ubuntu Server 12.04 (as an "always-on" Server), but ONLY on a Thumb Drive. Text only, cover closed, most access through ssh, though I would, occasionally open the Cover and use the Text Consoles.
Obviously, the Hard Drive was heating it up! (I eventually ended up, installing Debian 6 on the Internal Hard, and using it to Archive files, from other Computers. But still, mostly booting from the Thumb Drive).
Good luck with your Hardware!