If I write my own POS chain, from the genesis block, in secret, I can make sure that my chain doesn't have any/many double signatures ?
I can make it anything I like.. and obviously wouldn't release it until it had a greater 'V(u)' than the current valid chain.
The only way I know of choosing the 'valid' chain, if you can call it that, is by centralised checkpoints..
As for a punitive scheme, check out Slasher by Vitalik.. https://blog.ethereum.org/2014/10/03/slasher-ghost-developments-proof-stake/
As long as you can rule out a conspiracy involving 100% of historic inputs, you still have consensus.
Building directly on the genesis block is a special case because it involves 100% of historic inputs. If you built a fork directly on the genesis block, then 100% of satoshis would have double signatures by definition. Every satoshi would get blacklisted and the set of clean satoshis, Z_t, would be an empty set for all t>=1. There would be no consensus chain. It would be impossible for new participants to distinguish between competing chains.
So yes, you do need a checkpoint in this case, but the attack doesn't succeed if the objective is double-spending. And this attack is a bit unusual in any case. It is not very restrictive to have a single checkpoint some time after genesis. It is also possible to have a genesis block where inputs are divided across a wide range of owners. If you used an existing coin's current ownership structure to assign coins at genesis you would not have this problem.
If you built on the historic chain from a point where you don't control 100% of inputs, then we still have consensus. For example, say that one block after genesis the founder receives 99% of all inputs and some other guy receives 1% of all inputs. The founder does not have control over this residual 1% and uses his 99% to attack. If the founder kept his 99%, then he is supposed to win in any case. If the fonder spent any his 99% of inputs after this event, he could no longer use his historic 99% ownership to attack the chain. In this case, inputs he uses to SPEND on one chain and SIGN PoS blocks on another chain will be blacklisted and ignored completely for consensus purposes. Selection of the consensus chain woud revert to current holders of the remaining 1% of inputs (or some fraction thereof if some of this 1% has been blacklisted.) Blacklisted inputs are not part of the set Z_t. Therefore, blocks signed by these inputs do not contribute to V(u).
Finally, there is nothing punitive here so far. Blacklisting does not necessarily need to affect rewards for minting or the ability to mint blocks and send txns. So far it only matters for selection of consensus chains.