[Lizard]

iTunes syncing is really just for backing up a copy of your iPhone database. I can imagine a system where you could possibly use it to keep your data current on both Mac and iPhone, but it would require some scripting and yes, you'd need to be very careful to only use one of the two between syncs. I really don't recommend this.

An internal WebDAV server will be much easier (once it's set up) and much more robust. I think there may even be a couple guides on setting one up kicking around on these forums, depending on what servers you have available. This is probably the best solution, if you or your IT department is comfortable setting up such a server. (There may already be a WebDAV server on your network.)

Your third option would be Bonjour sync. In this setup, your Mac becomes the sync server for your iPhone. As long as you can get your iPhone on the same network as your Mac, this is probably the easiest to set up. And no data needs to go outside the firewall. Bonjour sync is available in OmniFocus sync preferences.