Do you actually know that Gnome is actively "code around" some alleged patent violation?
Programming around any imaginable patent violation actually seems really bad, especially given that software patents aren't looking as strong as they once were. I vaguely Linus or someone saying it's better not to research existing patents, it limits your liability. But just on the principle of letting corporations covertly bully you, it seems bad. It seems much better to force the companies sue you and see what happens.
My googling shows Apple has a patent on the App-bar but there are plenty of App-bars out-there. Red-hat apparently was worried to remove a dock but the screen shots we see here clearly show something like a dock. But even thread discussing that situation sounded murky. Docky still seems to be distributed for example.
Apple has patent on "Open Type" but that also is used heavily in Linux.