I've used the JTDS driver in production for around a year without any problems.
However, in your case, if you've got a system that been built and tested with the MS JDBC driver, then you really ought to stick to that.
In the meantime, conduct some tests and see if you can collect hard figures that show JTDS outperforming MS JDBC for your use cases. If the data back up these assertions, then come up with a plan to start using JTDS in your development and test cycles, finally rolling it out to your production release.
