Multiple external files for url rewrite under web.config
Can you use create multiple files (for development only) and create post-build rules that concatenate them all into the single rewrite.config file?
This way you can split them into multiple files and version control them during development and the post-build will aggregate them into one file for production purposes.
Does the second domain point to the same application in IIS? If they are different applications you could use the config transformation capabilities of VS to have a single file per domain and only deploy the file you need on each application:http://www.hanselman.com/blog/SlowCheetahWebconfigTransformationSyntaxNowGeneralizedForAnyXMLConfigurationFile.aspx