The force of friction is a macro force which describes the actions of many smaller forces.
These smaller forces are the electromagnetic interactions between the molecules, and these forces ARE conservative. However if you had a piece of graphite that was 12g, there would be 602 trillion trillion trillion (6.02 * 10^23) atoms. Even though only a small fraction of these would be the ones touching the other surface, there is still way to many individual interactions to calculate.
In these individual interactions the force is not in the same direction for each atom, so individually the atoms will instead begin to vibrate in random directions. There is energy in these vibrations, so the work done increases the vibrations of the atoms, and we call this heat.
However, if you summed up all the forces on all the atoms, you would find that there is a force which resists the motion of the collection of atoms as a whole. This force appears to be non-conservative because the random vibrations of the atoms cannot be converted back into a velocity going in the same direction, which would result in the collection increasing its speed.