Right now there is not a way to modify the top bar color in Tableau Online or Tableau Server - this specific color change was included in version 10.0 along with other layout changes.
As you mentioned, the site logo is the only customizable feature at this time: http://onlinehelp.tableau.com/current/online/en-us/to_custom_logo.htm
The best way to provide feedback on the current design and future enhancement would be to post in our ideas forum: http://community.tableau.com/community/ideas. Posting there will allow other users to vote and discuss the request, and will also help out our devs in gauging demand.
Hope this helps!