You just pushed problem one step back. All you have to do is start from known superblock and proceed to next one which can be arbitrary and then wait util txn between this blocks are forgotten. It is impossible to overcome this "problem", but it isn't any problem in real world, because very deep reorgs are not expected to happen and if they do community wil react anyway. Imagine bitcoin was attacked today with chain making 10000 blocks reorg and cancelling all txns. What would happen? Of course coummunity will apply patch with checkpoint cancelling this emerged fork.