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From your description, I'm not entirely clear if the performance issues you are experiencing are with the draw time of the feature class within ArcGIS or with the process of deleting and inserting of records. Perhaps it is both workflows that are yielding slow behavior.
Two quick questions come to mind right away:
Is the performance of your non-SDE source data the same, better, or worse than that of the SDE data you are describing
In thinking about the complexity of your polygon features, do they have millions of vertices or only a few per polygon
When connected to your Edit version (which is assumed to be a child version of Default), use the Truncate GP tool to wipe out the records from your polygon feature class. It sounds like you need to clean it out entirely, but correct me if I'm wrong here. Truncate works much more efficiently than a delete operation, but doing this will immediately commit your transaction in the RDBMS without the ability to roll back.
You can use the Simple Data Loader tool in ArcCatalog or the Load Objects tool in ArcMap to insert the records from your non-SDE source into your target geodatabase. Make sure you're connected to your Edit version when doing this.
3. RECONCILE / POST
Since you loaded data into the Edit version, those changes need to be "moved" into the Default version using the reconcile and post tools within ArcGIS Desktop.