What is the best course of action when attacked by a higher level commander and his army?

Power up and join a good corp. You can teleport away.

Only thing you can do is shield. Joining a strong corp will help keep you safer but it is inevitable, you will get attacked by stronger players, especially during deep battle event. So always have Aegis ready to use

Aegis when they are marching to attack. Heal your troops. and use marching speed ups to get back to their base and hit them as hard as possible(since they will be less defended)... then teleport away or aegis again...

Get reinforced. Have members in your corp evenly split the amount of reinforcements you can hold. More rein means more available rounds of battle in the attack against you which gives you higher chance of winning. Each unit type equals one round of battle.