Sorry for the late reply (2 years), but I recently bumped into this, and came up with the following solution.
The solution for SSRS 2008/2008R2/2012 is to use CSS to alter the rendering of the page.
1) Edit the following file: ReportingServices.css, located at C:\Program Files\Microsoft SQL Server\MSRS.[Instance Name]\Reporting Services\ReportManager
2) Line to be added just before the "body" specification:
3) Save the file, and create a new file in the same directory called "customization.css".
4) Place the following in customization.css:
background: url("../images/your_new_logo.jpg") no-repeat;
5) Add your replacement logo in the C:\Program Files\Microsoft SQL Server\MSRS.[Instance Name]\Reporting Services\ReportManager\images directory. Be sure that it matches the name and size that you specified in customization.css.
6) Bring up the SSRS web page and enjoy! This solution works well because it will preserve all of the positive customizations that can be performed via the web UI, and is minimally invasive on the back end.