I implemented a solution for this, if you get the latest svn trunk code you can specify different profile config files per site in Web.config/user.config like this:
<add key="mojoProfileConfigFileName-1" value="mojoProfile.config"/>
<add key="mojoProfileConfigFileName-2" value="mojoProfile2.config"/>
<add key="mojoProfileConfigFileName-3" value="mojoProfile3.config"/>
where the -number part of the key refers to the site id
Best,
Joe