Its pretty common to get dust in a 5D MK II above the focus screen. You can remove the focus screen and possibly blow it out and down into the mirror box where it can get on the sensor. The focus screen is easily removable, but use the proper tool to hold it, and never touch it, or it will get oily fingerprints which virtually cannot be removed.
Its better to ignore the dust, but I know thats difficult to do.
Yeah, after a little a bit of research I found various articles alluding to the fact that the 5DII does seem to be prone to catch dust. There's a thread on this forum that states the same. And you know, if this had happened after 6-12 months of heavy use, I would probably feel less precious about it, but as it's new, I want to keep it as perfect as possible.
Thanks for your thoughts and feedback!