I'm not entirely clear on what you are trying to do - I'm assuming that you are designing the main device, and want to use 'consumer grade' for want of a better term devices as peripherals.
Presumably this device attaches to the patient, and should ideally feature a USB port for monitoring etc. I'm not entirely sure why you specifically need to isolate the USB port - is it because the USB controller would have to share the same supply and communicate directly with the patient connections?
I've not seen any opto-isolators fast enough which I would feel confident would work at USB speeds. For this reason, the only solution I can come up with is to move the isolation point - at this point you have control over bus design and can use as many parallel lines as necessary to provide the required bandwidth whitout having to compromise the strength of isolation.
Would it not be acceptable to put the isolation barrier between your device and the USB controller, instead of between the USB controller and the bus? I'm not closely familiar with the regulations for medical devices, is there a clause that states that this would not be acceptable? Or would this option be to difficult to design in?