sorry, but that cracked me up sooo bad. I thought back to that picture of thermal paste cake on the top of an Athlon XP processor. The entire top surface was caked with silver thermal paste, the guy took it back to the computer store and demanded a refund cuz his processor didnt work. Man, if it were applied between the pins, this would have taken the cake.
Anyway, on a more helpful note. Thermal paste is to help thermal transfer between the CPU and the heatsink. No surface can be perfectly flat. There will always be micro hills and vallys on the surface of the heatsink/cpu even though it looks perfectly flat to us. For optimal thermal transfer, the largest surface of the base of the heatsink and the largest area of the top of the CPU have to be in contact. With bare metal on metal contact, the micro bumps and curves on the top of the heatsink result in a very small area of contact between the heatsink and the CPU, thus, poor thermal transfer as the area that dont touch because of the micro hills and vallys are filled with air, and that's a very good thermal insulator, to put it simply, bare metal to metal contact will result in a very hot CPU because the heat isnt going into the heatsink and it's trapped on the CPU.
Thermal paste is put on the area of the CPU that contacts the heatsink (in your case, the entire top of the CPU) and that fills in the micro hills and vallys, substituting air as thermal paste is a very good thermal conductor, making sure there is 100% contact between the CPU and the heatsink.
As some thermal pastes are also electrically conductive, if you put it in the pins, that will short alot of pins and render your CPU into a very expensive paperweight.