I'm a bit surprised by this. The solr URI should be configurable at any level.
I'll give this setup a try, and I'll let you know.
On the other hand, remember that you can by default index completely different sites in the same solr index, as the (site specific) site ID will by default be used to filter out search results.
On a more generic note, we usually recommend not to use the same ezp setup for multiple sites unless they're actually related (common design items, for instance). If the websites are related, being able to run cross-site searches is actually a good option. If no relation exists, it is much easier to maintain the sites separately.
Thanks for your suggestions Bertrand. Yes, in my case the websites are related and for this reason I chose the same ezp setup. Now that I know than eZFind adds the SiteID in the search query, I prefer use the same Solr core. But, still remains the issue related to the per siteaccess configuration of the solr.ini file. Please, update this ticket when you confirm this is true and I'll post a new issue in the eZ Publish tracker system.