Aaron,
Since drupal multisites really access the same repository (typically, of course you can have multiple repositories, but most people just go for one) in order to discern which objects are available/accessible to which multisite, the most common approach is to enforce namespace restrictions on the islandora module.
That way you can make some PID's being available to your root site, others to another. OAI module makes use of this, but, looking at the code at
It only works if you also filter the islandora namespace... ? Not sure if this is an error or a feature really, but my quick inspections says you need to enable "Exclude objects within the "islandora" namespace" in the OAI config form which will of course also lead to not exposing any PID starting with islandora:
Best
Diego Pino
Metro.org