I come to you from the future!
All joking aside, issues such as these were places where Splunk themselves realized the limitations in summary indexing. It is a great tool for some things, but has some serious architectural gaps.
In the modern world - as of Splunk 6.0 or so - we use Data Models and Data Model acceleration in order to achieve the performance advantages of summary indexing without all of the operational downsides of summary indexing. If you are still using Splunk (this is a 4 year old unanswered post afterall) - then the docs on DMs and Acceleration will give you a hint how to proceed:
http://docs.splunk.com/Documentation/Splunk/latest/Knowledge/Aboutdatamodels
http://docs.splunk.com/Documentation/Splunk/latest/Knowledge/Acceleratedatamodels
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