I don't know... the Phantom Zone was regarded as the ultimate punishment on Krypton, wasn't it? And with the planet about to go kablooey, along with anyone who could release the non-criinals from the Zone afterwards...
I remember seeing some Legion story that dredged up a lot of the trauma Mon-El underwent due to 1,000 years in the Phantom Zone. Jor-El may have seen it as kinder to let the Kryptonians die naturally.