Encrypt connection between SSRS and SQL Server
Unfortunately, you can't do this. 
There are two options (RSCM and rsconfig.exe) to set the connection string that SSRS uses to connect to the Report Server database and neither of them gives you the option to add the "Use Encryption for Data=True" parameter on the connection string. And since SSRS uses the SQL native client to connect you can't configure an ODBC connection and use it instead. The inability to set connection string parameters is definitely a shortcoming. I'm afraid you'd have to force encryption at the instance level to meet your encryption requirement.