From a pure hardware perspective, I would love to move this part of the service to Linux systems with GPUs. I spent some time evaluating this before we committed to the Mac Pro solution -- built some prototype hardware and did a cost analysis. It just wasn't the right move, because of the engineering cost for us. OS X's graphics pipeline is really strong, and we've built a lot of cool things with it. There is no analog whatsoever on Linux -- we would have to commit a lot of resources to re-build what we already have, and it would in the best scenario not be a customer-visible change. As a lean startup, we have to be ruthless with the work do: if it doesn't move the needle for our customers, it's probably not the right thing to do right now.
So instead, I've spent some time (and engaged with partners like Racklive) to get the Mac Pros to be as operationally acceptable as possible. This rack design and the chassis we designed go a long way towards achieving that goal. Airflow is taken care of, and the rack hits my power quota almost exactly (at full load). Cabling and networking and host layout follow our patterns from our conventional server racks. USB and HDMI ports on the front allow me to easily use a crash cart.
The lack of IPMI is my biggest operational headache. We have individual power outlet control and can install the OS over the network, so that's something at least.
The OS itself is also challenging. I'm not a fan of launchd. Finding legitimate information about how to do something on OS X is pretty tough, given that most of the discussions are focused around desktop users (who may be prone to pass on theories of how things work rather than facts). We've gotten it to a point where things work pretty well -- we disable a lot of services, run our apps out of circus, use the same config management system as on Linux, and so forth. We treat the Macs as individual worker units, so they're basically a GPU connected to a network card from the perspective of our stack.