I disagree with you that the design is wrong. I strongly believe that active defaults are the best way to reach good software.
The 128 default is set in IndexQuery, line 11.
The configuration system for Raven is RavenConfiguration, which is accessible from the callers of GetPageSize using this expression: Database.Configuration
You need to wire a new property and make it load the value from the app settings.
You'll be able to find samples of how this is done in the RavenConfiguration constructor.