Did the same thing you are thinking with the older Athlon Bartons XP-Mobile because they did not have a heat spreader - no issues. It is really useless since you want the core temp reads not socket ("surface") reads and speedfan can do that quite easily. Currently the A64s/opterons, Conroes etc have heat spreaders so you want to ensure that it is as flat as possible against the HS. What I do with my thermistor is place it on the HD or back of the Video card for lack of anywhere to put it.
I know the feeling - I have these extra wires and want to use it. My case have LCD displays for 2 fans 2 temps - I use them just for the displays which i do not even look at! Go figure