I just ran into the akonadi directory on my own system as well; it seem to be some sort of "personal information management" system that certain KDE programs rely on to provide random backend functionality. In my case, the program which seems to depend on this thing is k3b (a cd/dvd burning utility), though I haven't been able to determine what the interaction is between that and akonadi.
At any rate, in response to whether the folder in question is safe to remove: since akonadi is a KDE application, unless you plan on using any other KDE applications, there should be no problem whatsoever getting rid of the folder - and should you decide that you do need to use some such application again in the future, I have no doubt that akonadi will happily re-generate that folder for you, if need be. You may loose some saved program settings, but I'm pretty sure that's the worst you can expect to happen. Most programs seem to be pretty good about handling missing config directories.