Solution: Using mod_rewrite and mod_setenvif we can create rules to avoid logging these errors:

RewriteEngine on
RewriteCond %{REQUEST_URI} ^/index\.php/(.+)
RewriteCond %{REQUEST_URI} -U
RewriteRule ^(.*)$ - [env=dontlog:true]
CustomLog "/var/log/httpd/wiki-access_log" combined env=!dontlog

This assumes your wiki is in the top-level of a subdomain. If your wiki is actually hosted in a sub-directory such as www.mydomain.com/content/wiki then modify the RewriteCond to suit:

RewriteEngine on
RewriteCond %{REQUEST_URI} ^/content/wiki/index\.php/(.+)
RewriteCond %{REQUEST_URI} -U
RewriteRule ^(.*)$ - [env=dontlog:true]
CustomLog "/var/log/httpd/wiki-access_log" combined env=!dontlog