It should work by default...
That's odd; I just created a test project with MSSQL as the "--database" argument, and it added the JTDS driver to the POM:
This should work straight out of the box, as the JTDS driver is an open source SQL Server driver that's available from the public Maven repository. In other words, you should never have had to download or install the Microsoft driver. Are you using Roo 1.0.1?
"Now is the EJB of our discontent made glorious Spring"