So, I upgraded my site to wordpress 3.0 beta2, and giving it a try. I see that there is maintenance mode implemented to wp so it shows a warning site is in maintenance check back in a moment etc.
While updating plugins from my wp-admin, when it fails for some reason i have to go back and try it again. But, it shows maintenance mode warning when i refresh or go back to previous page. Each time i have to delete .maintenance from ftp so i can access to wp-admin.
So briefly, showing maintenance information for visitors may be a good idea (i think its not anyways), but it shouldn't block access to wp-admin when some problem happens about updating something. Or .maintenance file should be deleted when wp gives error.