I'd like to see this patch made too, but until it is...
It's not exactly correct to say that it "doesn't work" with RockBox, it just doesn't work the same. The cable from the Pioneer unit will still provide power and audio through your headunit, just not control. This means that you can still hear the iPod and charge the iPod through your headunit with Rockbox, you just have to use the iPod for control.
I actually prefer this because the iPod screen is much better than my headunit's. Get yourself a suction cup mount so you can have the iPod mounted in the lower left corner of the windshield.
This works with my 60GB iPod (5th Gen).