Probably, but it is conceivable that it won't or that the current version hardware will not work with the Apple USB3 chipset and that blackmagic will do a hardware change when they release the Apple USB3 drivers.
With Blackmagic stuff it is always best to wait until the features you want are actually confirmed as working, if you buy stuff now with the hope of some future update making it work then your likely to get burnt.
Blackmagic make all their hardware in very small batches, this allows them to easily make subtle changes to the hardware to enable new features (for example the hyperdeck shuttle 1 could not do DNxHD, they quietly updated the hardware and released the hyperdeck shuttle 2 when the compressed recording option was rolled out)
Hopefully the next Intensity IO will have dual thunderbolt ports for loop-through, and the USB 3.0 version will be Mac OS X compatible. That way people will be able to connect all their devices on a Macbook Pro without being limited by the end point only solutions. The retina-display MBP with dual TB ports doesn't have that limitation but you are limited in other ways; that's why I chose the non-retina MBP.