So, adding to the privacy pane and then removing caused a full index to take place, but strangely, while the indexing was being carried out, the fans didn't go that mental, in fact they weren't running very high at all. It was only when the indexing was finished that the fans ramped up again and the MacBook got really hot.
Next step was manually removing the .Spotlight-V100 folder, rebooting and letting it index again. Exactly the same result.
So it's not the Spotlight indexing being performed that is doing this, it's something funky going on with the finished index itself.
The only thing I can do at the moment is to keep it my boot drive in the privacy pane until a fix is released.