How much data are you moving through ODBC?

Unless you are expecting very large recordsets, you should be fine. If you are moving a lot of data (and the definition of "a lot" varies due to server hardware and traffic) you might consider moving to another protocol.

I would recommend putting the database server to work, too. User defined functions and stored procedures are powerful tools, and you should be able to see if the data is already present by making just one call.

Perl handles SQL Server via ODBC pretty well, too. During a database conversion project, I was getting better performance using Perl and ODBC than MS Access and ODBC performing the same tasks on the same data on the same SQL Server. It was not fast, it just took less time. (And yes, in this case, ODBC was a lot more effective than DTS.)

Good luck!