I am not going to get into the differences between FDHS and "the government". And I know this thread, I sound more like one of those anti-government loonies as compared to the pro-CIS slant I usually have. I am reminding this to put my comments in perspective.
However, the government is losing its ability to intercept people's communications because of so many people moving from plain old phones to so many other modes of communication. They (the govt) can not afford to lose that (power), and soon there will be hooks in all mainstream (or rather ALL) communications for either the government to intercept on a need basis, or just a dump of everything to check when they need to. Most likely you are going to hear about this after the program is underway for 2-3 or more years.
How will CIS use it? Not for day to day processing ... to begin with. However, I would not be surprised if this got plugged in as part of FBI check. Now does the FBI care whether you are a polygamist and should not be a citizen. Maybe not. But if you have other warning signs, don't be surprised regarding what they could do. Will the FBI work with CIS? That seems to be the weakest link. There would not be an incentive for these 2 departments to work with each other.
End of conspiracy stories.