Applied Architecture Patterns on the Microsoft Platform

Architecture selection

SQL Server and SSIS
Benefits Easily deployed and extensible ETL tool Designed to handle batch processing of large files, exactly the task at hand No additional licensing costs comes with SQL Server Can be built and maintained by current staff	Risks Need to build sophisticated error handling systems
BizTalk Server
Benefits Provides for live, real-time analysis Can leverage BizTalk capability to send events to downstream transactional systems Enterprise-class hosting infrastructure	Risks CPU-intensive processes High database process overhead Additional licensing and capital costs Not clear if staff has the skills to support product

When all is said and done, this is exactly the scenario that SSIS was designed ...