Most of what is discussed here goes right over my head, i have to admit.
Something my common sense (allways dangerous to use in this kind of threats 
) tells me is, that it highly doubts the projectile even has _time_ to breake up. It hits the atmorphere at 60.000 km/s, not the 30ish km/s of your regular asteroid. How does the atmosphere interact with that, would the missile have time to even react in any way or would it be through the atmosphere before any effect can take effect?
Or would the atmosphere be like a brick-wall, turning the missile into a ball of plasma? And then what? Whould the plasma be stoped dead in it´s track (I doubt that) or hit the ground at a somwhat slower, but still very significant speed?
Just a few things I am wondering, perhaps more knowledgable people can enlighten me 
I'm gonna go with brick wall. A simple dynamic pressure calculation says that at 50 km altitude and 60,000 km/s, a projectile will experience a pressure of 1.95 TPa (TeraPascals) or 2.83e11 Psi. That's way, way above the strength of any material I know, and the density (which dynamic pressure is proportional to) is only .00108 kg/m3, as opposed to 1.225 at sea level. So the object will suffer mechanical failure in the high atmosphere. At the same time, 1.95 TPa will also slow down the projectile. If it has a sectional density of 10,000 kg/m2, the resulting acceleration will be 1.95e8 m/s2. That's a very, very large number, and that means a lot of heat will be produced.
If it takes the projectile .001667 seconds to traverse the atmosphere, and over that time the above acceleration is constant (both of which are wrong, but I'm trying to get a handle on how much heat is generated), then over that time, the projectile will decelerate by 325 km/s. For each kilogram of projectile, that amounts to 19.4 terajoules of heat generated. That's more then enough to flash-vaporize the whole thing, even if 90% goes into the atmosphere, no matter what it's made of.
I know that TransNewtonian materials might change the values, but to survive, an object would have to be orders of magnitude more durable then anything we can make today.
As for what the resulting plasma would do, I'm under the impression that it would rapidly expand, reducing sectional density and slowing down faster and faster, so that it stops in the upper atmosphere. The big problem would not be the projectile's momentum, but the energy it carries. I'm not saying that any of this would be pleasant to be around, but it's going to behave more like a high-altitude bomb then a physical projectile.
