Hi,
The scenario you describe would work if your BizTalk installation is behind the firewall, located in the same environment as Database B. The only thing that would matter is establishing the connection to Database A in Amazon Cloud, so that you can fetch the data from Database A into your Orchestration and transform it into a data structure on Database B, assuming that you use the Microsoft BizTalk Adapter for SQL Server in both connections from your BizTalk application.
Daniel.