Even if they don't care that they site id down they will probably care about the public opinion that a couple of script kiddies took down the site if a top US government agency.
True, it's probably little more then a coat of paint on it's house. That being said, they're probably paying more attention to those that just threw eggs all over it, and if they chose, to act accordingly. Not like there woudl be much that would stop them.
I agree with the coat of paint comment but if we have learned anything about government agencies or large corporations being hacked in the past it is that their Internet security practices can sometimes be painfully bad.
@Below and HBGary was a IT security firm after all...
The CIA should be relatively secure: they are an intelligence agency, after all. Breaching a intelligence agency's website will cause the agency to lose more face than a Senator does after his or her website is hacked.