How do you address the problem where you get impossible superpositions that are difficult to resolve via repulsive forces, leading to a massive deposition of energy in the objects?
Cap the forces and/or trigger a more refined resolution mechanism, and maybe also force set the objects in a plausible {position, velocity}. This kind of simulation is by definition an approximation. You can detect impossible superpositions because they result in impossible forces. This is of course not applicable to the general case, so it depends if you want realism racing or massive unit count RTS physics.
http://i.imgur.com/ZgMNXpS.gif