Hi,
here is a link how you get rid of it and your layout isn't meesed up at all: http://www.themelab.com/2010/02/27/hide-the-wordpress-stats-smiley/
You have to give it a width and height of "0", set the overflow: hidden and make it positioning absolute, then you don't have the line at the bottom anymore.
NEVER make ist display: none, because then the Jetpack Stats don't work anymore.