I don't have anything to test this with currently, but could you not just create a new SQL connection, using an Existing Connection String, and add the Encrypt=yes option to it?
Driver={SQL Server};Server=MyServerName;Database=My_DBName;Trusted_Connection=Yes;Encrypt=Yes;
I feel like if you have a working connection string that works fine on the server running VisualCron uses the Encryption, you might be able to use it within VisualCron by doing that.
Brian