Relativistic math: KE = mc^2 (gamma - 1) where gamma = 1/sqrt(1-(v/c)^2).
Gamma is about 1.15 for 0.5c. The kinetic energy of a sidewinder missile (example I could find on easy google) would thus be gamma * 1/2 * m * v^2 = 0.577*m*v^2 = 0.577*83.5*0.25c^2 = 2.6x10^18 J. That's on close order to a 300 MT (1 ton TNT ~ 4e9 J) nuke (about 1.5 times larger than the largest nuke ever built). Cataclysmic for a country, but not "strip the atmosphere."
If we increase the speed to 0.7c, the energy only increases by a factor of 2.5 or so.
At 0.9c, you're up an order of magnitude (ie 3 gigatons of TNT). Ouch.
Edit: had the mass of the missile wrong, changing things by about a factor of 1/2.