Is there anything we can do across the company to make sure USBNinja and other similar USB cables that looks so real for users can really be mitigated?
USBNinja exploits design-level weaknesses of the USB specification. As such there is no simple technical solution and it is unlikely that one will emerge.
You can attempt to close down your USB using device control solutions, but a) you need a very homogeneous IT environment to be able to do that effectively (i.e. blocking devices based on vendor and product ID) and b) a targeted attack can easily work around these.
You also cause yourself headaches with device control that should not be underestimated. We've just been through this process for a customer, and it took days to find a tight policy that doesn't lock down the entire system (due to the way Windows loads its device drivers, if you block an essential device, your system is toast).
An awareness approach is most likely the one with the highest contribution to resistance, but it will also have holes (guests and visitors, contractors, etc.)
For your most valuable devices, I would seriously consider glueing known-good devices to the system at least so much that any tampering will be visible. Also lock unused USB ports (there are USB locks).
Consider USB locks also for notebooks of critical personel.
Update your training and HR policies to tell users not to plug things into the USB ports on their computers.
Anyone caught plugging something into their computer not on the official list gets a written warning with HR.
Buy a NinjaUSB yourself, write a payload that just sends an email, then leave the cable out and see if anyone bites. If they do, make sure you use it as a teachable moment.
Write a windows group policy to disallow USB devices such as badusb/NinjaUSB from registering when plugged in. Unfortunately blocking USB devices is a blacklist and not a whitelist approach. http://technet.microsoft.com/en-us/library/cc731387.aspx
EDIT: This site contains a list of known USB devices. You could write a script to block all those devices. https://usb-ids.gowdy.us/read/UC/. While it's not exhaustive, even a partial block list will prevent the unsophisticated attacker who purchases off the shelf hardware.