The jailbreak developer has answered yes to this question, and he also made a tweet pointing towards a YouTube video this morning that shows a tweak coming up for the device. It looks like it will allow protection of separate apps from Touch ID feature.
Check out this video:
While we already have seen several tweaks that are meant to protect the password, this will make use of the Touch ID feature for protecting apps. Also, the video shows that jailbreak developers have found a new line to work on, as was the case when Siri was released with the iPhone 4s. It will be quite intriguing to see what the developers come up with.
There is no word on when this tweak is going to come out, but it is a sign of things to come and they seem good.