Using Systems to Avoid has always worked for me. The only workaround I've found is to specifically tell a ship to warp into the restricted system, then give it orders for whatever it's supposed to do after that.
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The Unpronounceable Krsqk
"Well, sir, at the moment my left processor doesn't know what my right is doing." - Freefall
I've seen ships fly into systems set to be avoided that are ordered to go somewhere on the other side of the galaxy. It works sometimes, but not every time. And, sometimes I wan't ships to avoid a particular WP in a system, not the entire system itself.