She had ZERO interaction with her son. I mean.

Also why didn't she get punished due to natural born? It was not explained.

The story could have been handled much better like:

Lara was part of Zod's legion as well, she got sent to Phantom Zone as well due to her natural born.

As co-commander, she partially agreed to invade earth to bring back Krypton. But then she saw her son. Instead of Jor El, let Lara help Lois and Clark to get away.

Also instead of everyone got sent back to Phantom Zone, let Zod get killed first, then Lara and the rest of the Kryptonians agreed to leave earth to find a peaceful place to live. Before leaving, she wishes her son the best.