Maybe Twilight will sacrifice herself to destroy it!

@Background Human  
And the Terrans looked on in awe at first, as a solar eclipse enveloped the state of Missouri. Awe, however, soon turned to fear, as the sky continued to darken and the corona was swallowed up, piece by piece. The planet rotated underneath the shadow, resulting in a rising population witnessing the shadow of the moon grow every hour.
 
Less than two days later, the twin companion of earth smashed into the North American continent.

I can’t imagine twi having too much trouble with this. Teleport it away, push it off course, turn it into hay burgers…

 
 
a pure fusion device would still produce radioactive tritium and carbon-14

After five years, the tides of war have turned against the Terrans. In their desperation, they deploy the one weapon they had vowed never to use. A salvo of ICBMs, pointed directly at the heart of Equestria. It takes every ounce of strength for the alicorns and the Unicorn Corps to defend Canterlot from annihilation. But the missiles are a ruse. At 9:02 AM Canterlot time, just as the last missile is deflected, ten thermonuclear devices, parked in ten innocuous-looking trucks, simultaneously detonate, turning ten of Equestria’s largest cities into radioactive craters.
 
In their desperation, the ponies deploy the one weapon they had vowed never to use. Princess Luna is dispatched to Terra with a simple message: “Operation Moondrop is go.”

@chucklefarts  

 
Unicorn magic seems capable of pretty arbitrary transformations. Trixie and her teacups, Twilight turning an orange into a nest of bird eggs (that hatch!)…
 
Of course the simplest way to deal with a nuke is to just smash the warhead. Leaves a bit of a mess to clean up, though.

Step 1: destroy the guidance system with a precisely targeted magic laser. Now the missile can’t correct its course.  
Or: destroy engine bell. Now the missile can’t propel itself any further.
 
Step 2: redirect/throw missile to outer space, the bottom of the ocean, or an uninhabited desert. Whichever is convenient.

MISSILE STOP
 
TEMPORARILY
 
FUEL DECREASED, LEADS TO WARHEAD LANDING IN SCUM DESERT
 
NOT A SINGLE PONY IS HARMED

By just slowing it down with her magic she’s already totally changed the trajectory. Wherever it’s going now, it’s not going to its target.

@Phantom Rider  
But evil

@SuperPinkiePie64  
Let’s just say that magical atomic manipulation is cheating.

@SuperPinkiePie64  
Better yet, she takes the missile apart and retools it to a clean pure fusion bomb with no fallout and then sends it back. It’s much more powerful and wipes NK off the map while not subjecting the rest of the world to radiation.

@bugatti2005  
Well, that could allow her to prevent the nuclear detonation or create her own nuclear explosion.

@bugatti2005  
But glowing radioactive zombie ponies are cool.

@Background Pony #E717  
*missile
 
@Phantom Rider  
Not if she can send it to outer space (that if she can breathe like Batmane)
 
 
@chucklefarts  
Why manipulate tiny, unsignificant atoms when you can manipulate a 10-ton nuke missile?

Can her magic manipulate atoms?

Glowing radioactive zombie ponies!

atomic bomb