ORACLE: performance of query running across two schemas
Briefly, such an approach appears to me as a valid first step in integration process.  As long as the second schema is used for querying only, all its objects can be moved to readonly tablespace thus minimizing impact on backup time.  

You may or may not need to tune the instance, it all depends on how much load it adds to the database. For running reports, it should be safe enough to create resource profile (and use it) which limits CPU/Session time. Depends on your license, you can use Database Resource Manager which gives many more options to control resource consumption compared to profile.