Why would a government agency create a currency that undermines the government's ability to collect taxes?
For the same reason that a government agency would create a routing protocol that undermines the government's ability to censor and collect information.
The CIA would definitely be interested in a distributed, pseudonymous digital currency, in order to transfer money to assets. In order for such a system to be useful, it would have to be used by many other people (to provide cover) as well as be valuable (in order to be accepted by an asset for payment).
This isn't to say that the government as a whole won't be hostile to Bitcoin, but I think most government employees have a sort of tunnel vision.
Does anybody really think the CIA has any problem with fund transfers? Don't you think they already have plenty of methods of doing that and that it's extremely unlikely that Bitcoin (with all due respect) has come up with something novel that surprises them and gives them some new capability that they simply don't have already? Sounds farfetched to me.
To the extent that government agencies had anything to do with developing the software for the Internet, I suggest that 1) we can see how primitive and chronically insecure much of it is relative to the results of a blank-sheet effort today and 2) the government at the time had far less understanding of the consequences of the Internet.
My thinking is that the June invite is the opening act of their dance to get engaged with the people of this project in order to ultimately "persuade" them to provide some "backdoor" method of weakening the system so that it becomes ineffective as a defense against government. Surely they have the source code and the ability to understand this 100% on their own. Why even talk to Bitcoin people?
Here's a bargaining chip...
"If you want the power to find _real_ criminals who are using Bitcoin, then show us the _guarantee_ that merely _political_ crime such as tax evasion is exempt from any action by government."