There is no way of doing this via the WCF-SQL adapter. We have had to go with an external helper class to create the connection with a connection string and query the database.
Update: A Blog written by a colleague on the issue Can I use a BizTalk WCF-SQL send adapter with a SQL 2012 Always on Database? a snippet quoted below.
In summary I think your choices are (in order of preference):
Disable AlwaysOn Availability Groups / Mirroring on SQL server if you need to connect to this SQL server which has this enabled
Disable transactions and implement logic to be able to handle duplicates .
Disable transactions and handle the duplicates or lost messages with custom logic (e.g. Send twice and compare and implement error handling). You need to write your own DTC handling this which is probably very complicated.
Disable transactions and live with risk of duplicates or lost messages without handling duplicates.