I have added the ability to disable trading per each market individually in the exchange extension version 0.5.3-beta. You will find the functionality at the “Markets” tab.
About the other functionality you requested, I have implemented it as a separate extension and will release it soon. It will be possible to disable withdrawals and internal transfers individually per coin. It will not be possible to disable deposits, as these are external to the system.
Thank you for your suggestions, these are features that I believe will be useful to a large number of users.