In the Man Of Steel movie, the way Superman gets rid of the kryptonians aside from General Zod was by having them sucked into a black hole . Now we know after the destruction of Krypton , the phantom zone came apart releasing all the convicted Kryptonian criminals. But it does not mean that the zone itself was destroyed . So when the kryptonians are sucked into that black hole , will they be pulled onto the zone again ? Feeling a bit silly while asking this question , but the answer may be worth deliberating .
The Phantom Zone villains in Man of Steel were not "sucked into a black hole," though it may look like they were. Instead they were sent BACK to the Phantom Zone via the activation of a Phantom Zone Drive used by Jor-El to send Kal-El to Earth. The Phantom Zone was also the prison the Kryptonians were sentenced to before the destruction of Krypton.
In this clip you see the Phantom Zone drive activated by the crystal and driven home by Professor Hamilton (who is also lost to the Phantom Zone along with the Kryptonians.) When their airplane crashes into the Kryptonian ship, the Phantom drive is activated and creates a temporary singularity-like event which squeezes the Kryptonians back into the Phantom Zone.
Later in the film, it is revealed that the vessels Zod and his army are using possess a "Phantom Drive", a collision from a smaller ship (piloted by Col Hardy of the U.S. Military with Kal-El's rocket and operated by Emil Hamilton and Lois Lane) with a similar drive causes a cataclysmic reaction that creates a small singularity, returning the ship and its occupants to the Phantom Zone, along with the Military plane, Hardy, and Hamilton. The mere fact that a couple of Kryptonian ships are needed to create a window into this zone shows that it's not a naturally occurring prison. As previously stated we can assume that it's most likely much like the Phantom Zones in other media.
The film's official novelisation concurs with @Thaddeus' interpretation of events. The Kryptonians were sucked back into the Phantom Zone through a singularity. The transition, combined with the destructive effects of the black hole were sufficient to kill the Kryptonians (and any human captives) before their remains were deposited in the Phantom Zone.
Only Jax-Ur truly understood what was undoing them.
Of course, he reasoned. Kal-El’s original starcraft. They’re using it as a weapon against us. He smiled thinly. How ingenious.
The Black Zero had been designed to make the transition to the Zone in one piece, but only under strictly controlled conditions. The ship was meant to pass through the Projector, not have a Phantom Drive rip open the continuum right in the middle of the ship. Violent dimensional fluxes were already taking it apart before his fading eyes.
Solid bulkheads and supports sublimed away, causing the ship’s myriad chambers and corridors to cave in on themselves. Matter phased into energy, sliding between dimensions. The entire ship was collapsing into a singularity, or so he theorized.
His calculations did not spare him — or any of the others.
The singularity was approaching critical mass, pulsating above the city like a voracious black sun. The Kryptonian prison ship had been crushed into subatomic particles, leaving behind a sucking wound in the fabric of reality.
A deafening roar, like an extra-dimensional tornado, bellowed from the depths of the aperture. Blinding flashes of phantasmal light offered glimpses of a weird, purgatorial realm that was never meant to intersect with ordinary space. It made Lois queasy just looking at it.
Superman flew away from the vortex, pulling against the relentless forces that were trying to suck him back into the Phantom Zone with the other Kryptonians. Spectral colors glowed beneath his skin. His face rippled and distorted alarmingly; Lois could tell he was fighting with all his might to get them both clear of the singularity’s event horizon, before he was lost forever.