[1] - https://www.theregister.co.uk/2016/02/01/sgx_secure_until_yo...
[2] - https://www.corda.net/2017/06/corda-sgx-privacy-update/
[3] - https://invisiblethingslab.com/resources/bh09dc/Attacking%20...
Permissions are not tied to AAD members per se - we rely on a set of X.509 certs that correspond to the identities of the actors on the network for network-level authentication. These certs are referenced in the network constitution.
Ledger- and app-level authentication can be done however developers would like to do it. It can be, but need not be, AAD. See my comment above or the whitepaper for more details on the confidentiality design.
The biggest and critical issue with private blockchains is at the political level: how to make a lot of parties (e.g. bank) agree in a protocol involving critical things (e.g. money).
That said, there are some compelling scenarios that customers are exploring where a decentralized model opens up new market opportunities, or reduces risk or reduces cost.
One challenge with a database is answering the question of who operates it, and whether that party could choose or could be compelled to act maliciously. Coco and its ilk are specifically designed to address that concern, with tradeoffs in other dimensions as mentioned above.
In the technical whitepaper, one of the things we discuss is that the "Ledger Model" (data structures, APIs, abstractions and programming model) are owned by the ledger, not by Coco. I think you are right that using TEEs opens up the alternatives to some of the data structures and abstractions in use in the public networks today. We look forward to seeing what people will do with Coco in this regard.
It seems that permissions are set in each contract with identities tied to Azure AD members. I might be wrong about that. The white paper is pretty long and I only had time to skim it.