Can't say that I had an opportunity to compare the both. I might go for ODBC beacuse it would give some flexibility to read other sources. And I believe that nativity is not a problem since ODBC and SQL Server are from the same factory...
You might want to contact the institute for a second opinion.
two ways you can assign the library;
1. Via smc: you will need appropriate access. With this method you can control security etc.
2. The easiest way is to place the libref in the application server autoexec.sas file. Whenever a session opens, the library will be assigned. It will make it more difficult however to control security etc.