Yes, I'm aware of deterministic wallets and how they work cryptography-wise. It would work in cases where the determinism is permissible. However, a setup process where you have to write something down would be bad for automating. Electrum, supplemented with a printer interface which blocks until the key has been printed out could work. But I understand that there is no ready-to-use solution yet which automates the process of having keys securely synced before being used on the network.
The writing down seed step is merely in place for human backupability. If you were to code a separate project that would automate wallet creation for some kind of script... a la bitpay's merchant address generation script etc... you wouldn't need to write down anything and you could store the hex seed encrypted and not even bother with making it into a mnemonic.
I am not quite understanding what you are trying to do.
I also don't really understand your main concern either... but I think if you tell us what you are trying to do, we will be better equipped to assist you.