Originally Posted by
pinniped
If there's no fraud or anything unscrupulous going on, why the need for secrecy?

I've already assumed that someone on top-secret government work wouldn't be on Flyertalk asking this question, and would already have the credentials needed to travel with an alias.
I would ask the opposite question: Why can a person not have privacy and anonymity when choosing where to spend their money?
You might argue that a hotel needs your identity to guarantee you don't, say, smash the place to bits, but there's other ways to handle this situation (say a third party that covers liability for a member) without compromising privacy.