My threads are about as rusty as you can imagine. But when I put the rod in (with a bit of teflon tape), I snug it up finger tight and then give a little snug "umph" with a socket. Never leaks. The rod will never go all the way in. As said above, the hole is tapered.
Also, if you do wire-brush it down, it will just rust up again. And then you've got rust particles inside your water heater. You'll want to follow up by flushing out tank so those rust particles will not come on through your system. Granted, they will probably get trapped at your faucet filters.
Edit: I'd NEVER use any kind of chemicals to clean the rust off. You run the risk of deteriorating the metal threads, and getting chemicals inside your tank.