When running a hidden service the same precautions should be taken if you were running it over DNSstandard TCP/IP. Assuming the service is configured correctly then the only added risk is the Tor client implementation.
Depending on your resources you may want to setup a box only for the purpose of running the Tor client and pointing the service ports to another box running your service. Then block all traffic otherwise to and from that host by some means not controlled by the box running the service. (periodically reloading with an updated OS would be advised) If you don't have the ability to run two machines you could always virtualize that setup, something like ESXi would be great for such a setup.