Adafruit CC3000 Wifi Shield on IRQ 2?
It is a "hardware bug" as you so aptly put it. As far as I know, the only way to get the CC3000 board to use pin 2 as the IRQ is to physically rewire the connections. I did exactly that on my board and it works without a problem, leaving pin 3 free to use for whatever else you want. You can see what I did here.
It basically involves cutting the trace wire and running a jumper cable between the holes next to the pins.

The important thing to understand perhaps is that pins 2 and 3 are available to use for IRQ on the Mega and Uno, but it is an actual dedicated pin on the CC3000, hence why you have to go to this effort to change it. Also remember that once you have cut the trace to pin 3 it becomes an open/free pin and is no longer connected to the wifi shield. By the sounds of your requirements this shouldn't matter, but it is still useful to know.

If you haven't already, I recommend that you read the documentation for the CC3000 board, as it really helped me understand the irritating intricacies.

But yeah, if you choose to follow this and reroute the pin, it works perfectly. Hope this helps, even if it is a bit late.