The good news is that it won’t, at least to a certain extent. According to an email a user sent to Apple and obtained by MacRumors, Apple’s software chief Craig Federighi said that there will be some level of functionality, and that by running Boot Camp it will simply display the function keys that were removed as a result of the feature.
However other than that, it seems that is all it will be able to do, although it is unclear if developers for Windows apps will be able to take advantage of Touch Bar and offer up more functionality if they wanted to cater to Boot Camp users, or if Apple will release the API for Windows developers.
That being said, take it with a grain of salt since the email can’t be verified, but hopefully it is true since offering functionality, albeit limited, is still better than nothing.