The requirenment is to the siverlight web UI will define the CSV file format (i.e. first name, last name etc), the silverlight then need to publish the CSV definition to BizTalk as flat file schema. The Siverlight app does not need to be fancy, all it define is field name, field type.
My question is really how this process will work? The only way to me is to somehow generate exactly the same as visual studio does then use btsdeploy tool to deploy to management database.
Is there any more viable way to archieve this?
Based on the requirements in your question, there is no need I use BizTalk unless you just need it to take the silver light output from point A and transmit the output to point B.
The Silverlight app can easily output CSV or XML or whatever your final output is, assuming that the output does not have to adhere to some externally defined, complicated standard (HL7, EDI, etc.).