Einstein's famous equation has nothing to do with players colliding at different speeds. The "C" in the equation is not a variable, as you describe it, rather it is a fixed value equal to the speed of light. In short, this equation calculates the amount of energy that is stored by a mass ("M"). The famous use of this equation is in the design of nuclear power plants and the infamous use of this equation is in the design of nuclear weapons.
To go back to your analysis, a more appropriate equation is that of momentum. Momentum ("P") equals mass ("M") times velocity ("v"). P=Mv. The larger the momentum, the larger the force is required to stop or alter it (which brings to mind Newton's first law of motion, "A body in motion tends to remain in motion", unless it is me headed for the couch with beer in hand at Packer kick off time).
So, in your scenario where it hurts more to get hit by the smaller and faster guy, the laws of momentum and Newton say otherwise. There is no squaring of any of the variables, so they are equally weighted. That is, if the small attacker is half the mass (or half the "weight" here on Earth) of a bigger attacker, he would have to run more than twice the speed in order to "hurt more".
Me? I'd be knocked senseless whether J. Bush hit me during a light jog or Jolly hit me while reaching for his Gatorade. Laws of momentum won't matter much in my case.