Rusting is treated as good for bonding between steel and concrete as long as there is no scaling on reinforcement bars.
If the scaling of reinforcement bar seen, it indicates the heavy rusting of steel happened and you need to clean it out in order to ensure bonding of steel concrete.
You can remove the rust by using rust remover spray which is available in market, you can also get done this job manually by deploying labours.
From your picture it look like scaling of reinforcement happened and you need to remove all rust from them before concreting.
To avoid such scenario, if you know the concrete above that level is going to happen after a long time, you should get those bar coated with Anti-Rust coating which will prevent its rusting.