With a second layer, all the things I love about bitcoin vanish.
If you control the flow of money, you have power.
Indeed, the second layer is banking.
There are other second layer techniques like two-way-pegged sidechains (see Rootstock for an example) that are not censurable. They would preserve the actual transaction paradigm ("users sign a TX and get it included in a blockchain by miners"), only that the blockchain would not be the main blockchain but a secondary blockchain pegged to Bitcoin.
There are still challenges for sidechains (above all, the incentive system to ensure security) and the 2-way-peg needs additional Bitcoin measures, as far as I understand it. But I don't think it's impossible. For example, you could design an altcoin with a "bitcoin-pegged token" and a "mining token", and distribute the mining token to miners, while the pegged token would have a fixed supply. That design could work with Segwit and atomic cross-chain trading (ACCT is no science fiction, as it has already implemented in some small altcoins).