Handling logo changes through bugzilla and requiring shell access is a bit long. Instead we could set $wgLogo to Wiki.png for ALL wikis, shell access will no longer be required and communities will be able to change it quickly.
On new wiki creation, upload a default Wiki.png file and protect it. This can be handled by a script, and surely need an update of our wiki creation documentation.
Look at all wgLogo, contact the communities and ask them to switch to Wiki.png. Or we could use a script which move the existing logo, protect it and leave a redirect.